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266 Cards in this Set
- Front
- Back
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GLUT1 is present in which cell type?
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erythrocytes and have a high affinity for glucose (low Km)
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GLUT1 and GLUT3 are present in which organ..
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brain (low km, high affinity for glucose)
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GLUT2 is present in which organ..
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liver and pancrease (have a low km/varying affinity for glucose)
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GLUT4 is present in which organ...
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in muscle, adipose, and heart with intermediate affinity for glucose
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SGLUT1, unlike most glucose transporters act by what cellular transport mechanism?
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facilitated diffusion, co-imports glucose and sodium into the apical membrane of the intestinal lumen cell... maintenance of sodium gradient allows 'pulling' glucose into the lumen against its concentration gradient
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Draw the km v.s. glucose level for glut-1 and glut-2
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Describe how glucokinase facilitates the phosphorylation of glucose to glucose-6-phosphate
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* at low glucose levels it resides in the nucleus bound to a regulatory protein called Glucokinase regulatory protein (GKRP) which inhibits its activity
* when glucose concentration goes up, Glu-6-p or fru-6-p accumulation releases glucokinase from nucleus to cytosol *GKRP is removed and the free form of glucokinase can now bind to glucose or fructose |
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summarize what glucose does in the body...
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* reduces blood glucose by increasing uptake and utilizatoin in muscle and adipose tissues (Glut-4)
*reduces circulating amino acids and fats by increasing conversion to protein and storage of triacylglycerols, respectively *Incrases liver utilization of glucose by increasing rates of glycolysis (gk+pfk and pk) and glycogen synthesis *inhibits gluconeogenesis by increasing fru-26-p2 levels *increases conversion of carbohydrate to lipid (VLDL assembly and export) |
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describe the mechanism of insulin secretion ...
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ATP accumulation inhibits ATP-sensitive potassium channels in plasma membrane
* results in calcium uptake *this uptake results in fusion of insulin vesicles with plasma membrane and the release of insulin * |
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name 6 biochemical processes which insulin stimulates
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glycogen synthesis, glycolysis, amino acid uptake, protein synthesis, fatty acyl and cholesterol uptake
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where does glucokinase reside?
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liver
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Why is diabeties a problem?
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kidney damage - fatigue, damage to fine capillaries
*eye - blood circulation in the eye involves fine capillaries that can be damaged * nerve damage - occurs because of bad circulation * lack of insulin -an anabolic hormone- its absence results in failure to repair damaged structures |
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how does vascular damage due to diabetes happen?
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GLYCATION: hyperglycemia leads to non-enzymatic attachment of blood glucose to proteins, this modifies endothelium of capillaries making them less flexible and porous which results in bleeding
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how does diabetes cause cardiovascular disease
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because insulin (since lipoprotein lipase is induced by insulin) stimulates tissue utilization of fats and amino acids, lower insulin results in higher levels of fats in the blood, leading to heart disease
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absence of insulin results in...
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1)hyperglycemia, (due to decreased uptake, utilization, and increased hepatic gluconeogenesis)
2}hyperlipidemia (decreased uptake and utilization of dietary triacylglycerols and cholesterols (lower lipoprotein lipase), increased adipse lipolysis (increased triacylglycerol lipases), increased VLDL production, 3)ketosis due to incrased availability of fatty acids for heptatic ketogenesis and decreased peripheral keton utilization, 4)uremia due to increased proteolysis and amino acid catabolism |
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Pyridoxal phosphate is a co-factor in what three processes?
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glucose to glucose-1-phosphate, transamination of Serine DH and Threonine DH
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describe the affect of insulin and glucagon on pfk1
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insulin DEPHOSOPHORLATES PFK2 causing Fructose 2,6-bisphophate to elevate
glucagon cause cAMP levels to increase activating protein kinase A phosphoralating PFK which decreased F-2,6-BP |
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describe the affect of insulin and glucagon on pfk1
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insulin DEPHOSOPHORLATES PFK2 causing Fructose 2,6-bisphophate to elevate
glucagon cause cAMP levels to increase activating protein kinase A phosphoralating PFK which decreased F-2,6-BP |
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fatty acid degradation is regulated by...
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phosphorylated hormone-sensitive triacylglycerol lipase HSL) in liver/muscle mitochondria (stimulated by glucagon/epinephrine)
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fatty acid synthesis is regulated by...
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by dephosphorylated acetyl-coa carboxylase (ACC) in the cytsol of liver (activated by liver)
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glycogenolysis produces how many ATP and why
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3 atp because glycogen phosphorylase produces glucose-6-phosphate which circumvents step 1 in glycolysis and saves one ATP
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What is the pathway of glycogen breakdown in muscle
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Does not go to blood, Glycogen ->G1P ->G6P->glucose
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name all the enzymatic reactions where NH4+ is either a reactant or product
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1) serine -> pyruvate
2) threonine -> alpha-keto-butyrate (enzyme: threonine dehydratase) 3)glutamate + nh3 -> glutamine (using glutamine synthetase; how ammonia/nh4 is transported in the blood) 4)glutamine + h20 -> glutamate + nh4 (enzyme glutaminase; helps eliminate excess acid in response to metabolic acidosis) |
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where are bile acids (bile salts) made, stored, secreted, and reabsorbed
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made in the liver from cholesterol catabolism, stored in the gallbladder, secreted in the duodenum and reabsorbed in the small intestine
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adult humans produces ___ of bile daily, which are composed of ___,
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400-800mL, composed of bile acids, cholesterol, phospholipid, bicarbonate, and bile pigments
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how do cholelithiasis form?
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gallstones form when the gallblader is inflamed and the concentration of cholesterol increases in bile for any reason, the cholesterol solidifies the bile since it is not dissolved by phospholipids and bile acids. Gallstones are almost pure cholesterol
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generally describe the steps of bile acid synthesis..
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1) cholesterol modification into bile acids occurs though hydroxyl group addition
2) First committed step is the formation of 7-alpha-hydroxycholesterol by cholesterol 7-a-hydroxylase with cytochrome-p450 prostehetic group 3. cholic acid (cholate) or chenodeoxycholic acid eventually forms through a set of redox reactions. 4. these acids are made more soluble by conjugation in the liver to an amino acid (glycine or taurine) to yield bile salts |
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cholic acid has ___ OH groups
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3 OH groups
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chenodeoxycholic acid has ___ OH groups
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2 OH groups
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names 4 bile salts
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glycocholic, glyco-chenodeoxycholic, taurocholic, taurochenodeoxycholic acids
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what are the primary bile acids, what are the secondary bile acids
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primary - cholate, chenodeoxycholate; secondary - deoxycholate, lithocholate
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what are the differences between primary and secondary bile acids in how they are produced?
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1)primary bile acids are secreted in bile where they enter the intestine
2) Bacteria in the intestines remove -OH groups to form secondary bile acids |
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what is the physiological role of bile acids (three things)
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1 elimination of excess cholesterol, the main way to get rid of excess cholesterol
2 they faciliate the digestion of dietary triacylglycerols by actiing as emulsifying agents that render fats accessible to pancreatic lipases 3 they facilitrate the intestinal absorption of fat-soluble vitamins A,D,E,K |
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what is Bilirubin?
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the breakdown of heme which forms the pigment of bile
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how does bilirubin get into the blood?
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cholestasis (interuption of bile flow) causes "regurgitation" of bile acids back into the blood along with conjugated bilirubin caused by blockage or gallstones (cholelithiasis)
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bile acid sequestrants
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what prevents the re-absorption fo bile acids allowing them to be excreted into feces. This lowers the amount of cholesterol
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cholestyramine...
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inhibits dietary vitamin a,d,e,calcium, and iron absorption
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which is the only reaction in the body that creates carbon monoxide
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hem to biliverdin, measuring CO exhaled from lungs indicates the rate of heme breakdown int he body
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briefly describe the mechanism fo heme to bilirubin
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1. heme oxygenase converstes heme to biliverdin (produces CO; porphyrin ring opened up at the expense of NADPH and O2)
2. Biliverdin reductase converts biliverdin to bilirubin (outside liver, with NADPH) 3. bilirubin brought into liver cells by albumin 4. inside liver UDP glucoronyl transferase converts the bilirubin into bilirubin diglucoronide (conjugated form) |
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describe the process of bile excretion
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bile in small intestine lumen is conjugated bilirubin components are hydrolyzed by intestinal bacteria into urobilinogen
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what gives urine its yellow color
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urobilin
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what gives feces its brown color
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stercobilin (oxidized from uroblinogen, by bacteria)
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what is jaundice..
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any accumulation of bilirubin in the blood which leads to darker urine, a yellowing of the skin and noticalbe yellowing of the sclera
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what is the difference between unconjugated, mixed, and conjugated hyperbilirubinemaa and which "type" are they
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unconjugated - type 1 - decreased uptake
conjugated - type 2 - normal uptake but defecit in excretion mixed (hepatocellular) hyperbilirubinemia - type 3 - the hepato cytes are impared from alcohol abuse or some type of viral hepatitis |
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what types of unconjugated hyperbilirubinema is there...
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*exogenous - antimalarial drugs, favism, or botched blood transfusion
* congenital defects (glibert's syndrome) *infants born with immature bilirubin uptake |
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what types of conjugated hyperbilirubinema are there...
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*obstructive
*dubin-johnson and rotor syndromes |
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Describe how heme is synthesized..
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1. succinyl coa combines with glycine via delta-aminolevuliate synthetase (ALA synthase)forming delta-aminolevulinc acid
2. the delta aminolevulinc acid is transported to the cytosol to join with another forming a porphobilinogen monomer 3. for of these porphobilinogens come together to form a linear tetrapyrrole 4. uroporphyrinogen II cosynthase acts to close the linear tetrapyrrole into a ring shape, such that the resulting compound is asymmetrical 5. uroporphyrinogen II is converted to coproporphyrinogen III, which is transported back into the mitochondria 6. Following a few decarboxylations by oxidases, an iron atom can then finally ecome part of the porphyrin ring to form a heme, via the catalyic action of ferrochelatase, another enzyme sensitive to heavy metals |
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what is prophyria and what are the symptoms?
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porphyrin metabolism disorder: staining of body tissues, urine becomes red and teeth becomes reddish-brown, delirium and depression, skin becomes very sensitive to sunlight, fine hair can develop over the face and limbs,
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aldosterone is synthesized by the..
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thermoradiotherapyglomerulosa of the adrenal cortex
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cortisol is synthesized by
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fasciculata of the adrenal cortex
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androgens are synthesized by
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the reticularis of the adrenal cortex
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name some steriod hormones
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glucocorticoinds (cortisol), mineralocorticoids (aldosterone) and sex hormones (androgens, estrogens, progestins)
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what does aldosterone do?
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* stimulates Na+ and water retention by the kidney
* plays major role in maintence of blood pressure * regulated by renin-angiotensin system |
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wha is a Barr" body
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inactivated x-chromosome that coils up and dense
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Turner's Syndrome has what kind of karyotype
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45X0
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which ratio has higher occurrence ACTG dna and which bands are they
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humans have low G/C content which arelight bands
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dark and light bands are?
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light bands have higher GC content
dark bands have higher AT content |
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euchromatin v.s. heterochromatin
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euchromatin are open structures that contain genes that are amostely active
heterochromatin are highly condensed closed structures that consist mostely of inactive genese composedof mostly centromeres |
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p arm is q arm is and list facts
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p (petite) arm is the small arm (early-replicating, contains most genes) and q is the long arm (late-replicating, contains few genes)
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name three trisomies
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Trisomy 21 - Down's
Trisomy 18 - Edwards Trisomy 13 - Patau |
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a nondisjunction error is
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during meiosis the pair of homologous chromosome does not separate equally
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name the classes of chromosomal abnormalities
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deletion, ring chromosomes (breaks of ends of arms and anealing of each other forming a ring), duplication, isochrome (loss of p-arm and duplication of q-arm), inversion, translocation (reciprocal/robertsonian)
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pericentric v.s. paracentric
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pericentric - an inversion with a break in q and p arm
paracentric - an inversion with both breaks in same arm |
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reciprocal v.s. Robertson
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reciprocal - one break in each of the chromosomes, the two broken segments are exchanged (only pathological if breaks occur in coding region)
robertsonian - exchange of genetic material between two acrocentric (chromosome with its centromere located near one end of the chromosome) homologous and non-homologous |
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how does huntington's disease occur
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a CAG triplet is repeated (which codes for glutamine), and the number of repeats tends to expand in successive generations, leading to greater severity
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symptoms of huntington's
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middle age symptoms, unsteady gait, large polyq leads to protein aggregation and accumulation in the cell
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Fragile-x
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* only affects boys
* x-linked recessive *mental retardation *enlarged head an testes *involves CGG repeat |
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imprinting is..
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genes, or regions of genes, that are only expressed on chromosomes that come from father or mother
* you will have disease even though it is recessive |
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prader willi syndrome
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deletion on the paternal chromosom, hypotonia, hypopigmentaiont, hypomentia, hyperphagia, hypogonadism, almond shaped eyes, full cheeks
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What does cortisol do...
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* increases gluconeogenesis, lipolysis and proteolysis
* suppresses immune system aand Ca2+ GI absorption, so excess cortisol affects bone synthesis and can lead to osteoporosis * regulated through hypothalmic-pituitary-axis * interferes with initial step of arachidonic acid synthesis (asprin is atep below steroids in blockign this pathway and is less powerful pain reducer) * interferes with immune and inflammatory response |
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what do androgens do...
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* determine secondary sexual characteristics
*virilization (hair on chest, etc.) * regulated through hypothalamic-pituitary-axis |
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what do the catecholamines do..
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epinephrine and norepinephrine
* regulate glycolysis/gluconeogenesis under stress and excercise conditions * regulate cardiac rate and output |
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Which is the rate-limiting step of steroid hormone synthesis
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the conversion of cholesterol to pregnenolone catalyzed by P450 side chain cleavage enzyme
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What produces ACTH, what does it act on?
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Adenocorticotropin is produced by the anterior pituitary and stimulates the adrenal cortex
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describe the mechanism of ACTH
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acts n the adrenal cortex leads to protein kinase a activation via camp which in turn acts in two different ways to increase cholesterol inside the cells:
* it phosphorylates the LDL receptor to bring in more cholesterol * it phosphorylates cholesterol ester hydrolase (CEH) inducing it to increase the break down of cholesterol esters into cholesterol |
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cushing's syndrome
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(Primary Adrenal hyperplasia) excess acth - is caused by a problem with the adrenal cortex (such as a tumor) that results in excess cortisol production), High levels of cortisol and low leels of CRH and ACTH
Symptoms: hyperglycemia, muscle wasting, hypertension, osteoporosis, decreased immunity |
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Cushing's disease
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(Secondary Adrenal Hyperplasia)
caused by tumor in the anterior pituitary that reults in increased cortisol levels or anterior pituitary increased production of ACTH abnormally Symptoms |
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symptoms of excess cortisol
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initial weight gain, hypertension, later truncal obesity, moon faces, buffalo hump
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Addison's Disease
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primary Sdrenocortical insufficiency
* abnormally low levels of cortisol levels * often caused by autoimmune destruction |
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Secondary Adrenocortical insufficiency
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Can be caused by
*pituitary ACTH deficiency Hypothalamic CRH deficiency |
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Symptoms of Adrenocortical insufficiency
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*weakenss, fatigue, weight loss
*hypotension *salt craving *hyperpigmentation (excess ACTH --melanocyte stimulating hormone in ACTH encodes for and leads to excess production of melanin) *high potassium levels |
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Adrenal steroidogenesis
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caused by a cogenital defect in the enzyme CytP450-21alpha-hydroxylase
*the defect in this enzyme cortisol and aldosterone synthesis is blocked *remaning steroid hormone precursors are shunted towards synthesis of androgens |
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symptoms of adrenal steroidogenesis
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in women: hirsutism, acne, virilism, menstural irregularities
in chldren: precocious puberty in men: no serious clinical consequences |
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Where do the nitrogens and carbons from the purine rings come from?
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N1: aspartate
C2,C8: Formate (from THF) N3,N9: Amide N of gllutamine C4,C5,N7: Glycine C6: CO2 |
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why are pregnant women given folic acid supplements
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lots of DNA/RNA biosynthesis is going on in the fetus and THF is needed for the C2 and C8 carbons in purine
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Cdk2-cyclinA controls?
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entry into mitosis
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cdk1-cyclin B
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*anaphase promoting complex (APC) polyubiquitinates cyclin B in late metaphase so that it is degrated by the proteosome
* Degredation of cyclin B allows the cell to proceed through anaphase |
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in PROPHASE...
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poles of spindle appear and chromosomes condense and become indivicualized
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in PROMETAPHASE...
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nuclear envelope breaks down and chromosomes attach to spindles
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in METAPHASE
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all spindles are formed and chromosomes align on spindle equator (metaphase plate), after all spindles are attached AP is activated and the cell can move to anaphase
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in ANAPHASE A...
in ANAPHASE B... |
in ANAPHASE A sister chromatids separate and move to pole
in ANAPHASE B cleavage furrow assembles, organized central spindle assembles (marker for where to cleave cell) and poles seperate |
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in Telophase
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cleavage furrow constricts
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in CYTOKINESIS
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chromosomes decondense, interphase microtubule network reforms, and daughter cells separate
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how do subcellular membranes rearrange for distribution into daughter cells (for example the golgi)...
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Cyclin B-Cdk1 phosphorylates GM130 which prevents binding of p115 (on the vescile) preventing fusion of vesciles and triggering breakdown of golgi into vesicles
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describe the nuclear membrane rearrangement during mitosis...
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cyclin B-Cdk1 phosphorylates Lamin B, causing the meshwork to disassemble and leading to fragmentation of the nuclear envelope into vesicles and small membrane sheets, during reassembly a phosphatase removes the P and the meshwork reassembles
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Microtubules are made up of...
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alternating beta and alpha tublin
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tublin binds which nucleotide
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GTP
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describe the polarity of microtubules
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the alpha end of is referred to as the - end and the beta-end is referred to as the + end
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which end do microtubules grow or shrink from
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MTs gro or shrink from the + end
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describe the state of microtubles with when GTP is bound or unbound
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in the bound conformation, protofilaments are straight and can arrange linearly to form the microtubule
in the is unbound, mt is unstable and so MT will break down (changs the conformation, introducing kinks that prevent the formation fo organized MTs |
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MTs grow from
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a gamma tublin ring complex (a seed)
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what is the difference between centrosome, centrioles, centromeres
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centrioles - structure which gamma tublin is organized around
centrosome - pair of centroles centromere - region of DNA near the center of a chromosome |
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describe and name the three types of microtubulues
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kinetochore microtubulues - attached to chromosomes
overlap microtubuules - run past the chromosome and overlap with the ones coming from the other side astral microtubules - outside the spindle |
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when does and what condenses the chromatin
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condensin condenses the chromatin during prophase using ATP
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compare and contrast cohesin and condensin
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condensin links the same strand of DNA whereas cohesin links different strands (such as sister chromatids) cleavage of cohesin allows progression from metaphase to anaphase
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describe the process of sister chromatin separation
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1) kinetochores properly attached to MTs
2) Mad2 can't associate with kinetochore 3) Cdc20 can activate APC 4) APC destroys securin 5) releases active separase (protease) 6) degrades cohesin 7) sisters separate |
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how are MTs shortened in late anaphase (anaphase B)
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* motor proteins (kinesins and dynins) create movement
* overlap microtubules provide pushing force * astral MTs provide pulling force |
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what is the difference between chiasma and holiday junctions
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holiday junctions only involve a single strand of DNA, chiasma involves both
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how does genetic diversity occur in meiosis
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independent assortment and crossing over
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describe fertilization
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acrosomal region on sperm interacts with zona pleucida of egg releasing contents which degrades zona pleucida, membrane of sperm and egg fuse and sperm releases nuclear contents, at the same time cortical granules release hydrolytic enzymes which modify the zona pelucida to prevent multiple sperm from entering egg
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marfan syndrome...
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* very tall and thin with long arms ang fingers
* if the length of the arm span of an individual is greater than the person's height by 10-cm, there is a reason to suspect Marfan *Fingers can have a long, spidery appearance called arachnodactyly *curvature of the spine (scoliosis), abnormal indentation (pectus excavatum) or protusion (pectus crinatum) of the chest cavity *dislocation of optic lens (subluxatoion) upward and outward, as well as myopia (nearsigntedness) * auortic dissection - the inner layer of the aort's artery wall splits open |
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what is the difference between incomplete penetrence or variable expressivity
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incomplete penetrence - whether the trait is expressed or not
variable expressivity - the degree to which the trait is expressed |
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noonan syndrome
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1. physical manifestations: short stature, congenital heart defect, broad or webbed neck, unusual chest shape, apparently low-set nipples, developmental delay of variable degree, cryptorchidism in males, characteristic facies
2) cardiac complications: pulmonary valve stenosis, hypertropic cardiomyopathy, other structural defects (atrial and ventricular septal defects, pulmonary srtery stenosis and tetralogy of Fallot) |
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Williams Syndrome
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very rarely inherited, deletion on chromosome 7
*physical manifestations: short upturned nose, droopy face, blue eyes with a lacey pattern, high ca++ (hypercalcemia can cause seizures), hoarse voice, "cocktail type" personalit, elastin gene defect -> faces age more quickly, causes underlying cardiac defect |
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neurofibromatosis (1 v.s 2)
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_1_
*six or more cafe-au-lait spots * two or more neurofibromas of any type *freckling in the axilla or groin *optic glioma *two or more lisch nodules *dysplasia fo the spenoid bone *a first-degree relative with NF1 _2_ much less common than NF1, controlled by a different gene, usually causes hearing loss and acoustic neuromas |
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Osteogenesis imperfecta
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*aka brittle bone disease
*autosomal dominant disorder *high rate of coming about through spontaneous mutation after fertilization *not enough good quality collagen is made so the bones are weak and fracture easily, can possibly confuse disorder with child abuse *"robin's egg blue" sclera * usually, the thicker the sclera of the eye, the whiter it appears, in babies it is more blue, in children with OI, it is even more blue *discoloration and malformation of teeth, ltos of notching with age *hearing loss *can be an example of germline mosaicism |
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gonadal mosaicism
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two populations of cells with different genotypes within the same patient
a usually one population of cells is affected by a genetic disorder |
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name 4 triplet repeat disorders and their corresponding triplets
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Huntington's - CAG
Fragile X - CGG Myotonic dystrophy - CTG Freidrich Ataxia - AAG |
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fragile X
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*associated with increased CGG repeats in the FMR1 gene (located on the X chromosome Xq27)
* fragile X is the most common from of inherited mental retardation * characterized by moderate mental retardation in affected males and mild mental retardation in affected females * males often have abnormal facies, including a long face, large ears, prominent jaw * afffected females have milder features * normal range (5 to 40) * intermediate 41 to 50 *premutation (59 to 200) *affected rage over 200 |
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prader-willi syndrome is...
angelman syndrome is... |
prader-willi is a paternal deletion
angelman ismaternal deletion |
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Which enzyme is involved in the following reaction:
ATP + AMP = 2 ADP |
Adenylate Kinase
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Which enzyme is involved in the following reaction:
ATP + NMP ADP + NDP |
Nucleoside Monophosphate Kinase
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Which enzyme is involved in the following reaction:
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Nucleoside Diphosphate Kinase
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The outer mitochondrial matrix contains which protein.. and is permeable/nonpermeable
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TOM complex, permeable
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The inner mitochondrial matrix contains which protein and is permeable/nopermeable
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TIM complex and is nonpermeable which is important for maintaining electricochemical gradient
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most of the proteins in the mitochondria in general are encoded ...
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in the nuclear DNA rather than the mitochondrial DNA
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what is cardiolipin and where is it found
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a variety of phospholipids that creates "raft-like membranes" (very tight, non-permeable) it is found in the inner mitochondrial membrane
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mitochondria make how many ATP per second
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9E20
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Name 7 processes which occur within the mitochondria
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* TCA
* Electron Transport *Urea Cycle *Beta oxidation *sterol biosynthesis *heme biosynthesis *copper and iron homeostasis |
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The half life of Mitochondrial DNA and is how big and what shape and encodes how many proteins
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1 to 4 weeks, ~16kb, circular, 13 proteins used for teh respiratory pathway complexes (I, III, IV, ATP synthase)
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transcription and replication in the mitochondria start...
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in strands called D loop which happens bidirectionally (no need for okazaki fragment model in a cirucal system)
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most nuclar-endoced mitochondrial proteins have what localization sequence
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2/3s have a N-terminal localization sequence
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kearns-sayre syndrom is
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a deletion in a direct repeated sequence in the mtDNA, results in death of cells , most often presents as a stroke
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leigh's syndrome
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have little complex iv, cytochrome oxidase which is needed to make ATP and avoid metabolic acoidosis
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Mitochondrial Encephalopathy with Lactic Acidosis and Stroke MELAS, (and MERRF?)
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leucine tRNA gene is mutated
* only one mitochondrial tRNA for every amino acid; therefore can't make mitochondrial proteins properly symptoms: short stature, seizures, stroke-like episodes with focused neurological deficits, recurrent headaches, cognitive regression, disease progression, ragged-red fibers (MERRF, similar to MELAS but occurs in Lysine tRNA) |
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LHON: Leber's Hereditary Optic Neuropathy
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involves a point mutation in mtDNA for Complex I (NADH Dehydrongenase).
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KSS: Kearns -- Sayre Syndrome
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Normal is 16.6 kb of mDNA but large deletion (only 6.8kb total) in KSS
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|
what are the three symptoms of how mtDNA mutations arise:
|
* mtDNA polymerase-gamma is error prone (not true)
* mitochondria lack DNA repair ability * mitochondria generate ROS |
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|
describe the generation of ROS
|
complex 1 in the mitochondria spill electrons onto O2 forming superoxide (O2-) which removed by superoxidedismutase which is also damaging but is removed by GPX-I
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|
Describe Pyrimidine biosynthesis
|
* the rign is synthesized from glutamine by carbamoyl phosphate synthetase II in CYTOSOL
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|
what drugs inhibit thymaine synthesis and what enzymes do they inhibit
|
fluorourocil (fdUMP): structurally similar to dUMP, binds competitively to thymidylate synthase stopping the dNTP synthesis pathway,
methotrexate, aminopterin - irreversibly binds to dihydrofolate reductase |
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|
xanthine is converted to uric acid by which enzyme
|
xanthine oxidase
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|
what drug is an irreversible competitive inhibitor of xanthine oxidase
|
allopurionol
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|
|
describe how gout occurs in von gierke's disease
|
G6P accumulates -> shifts to HMP -> ribose-5-phosphate accumulates -> leads to increase in PRPP and stimulation of purine pathway -> overproduction of purine -> increase degradation -> gout
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|
purine nucleotides are degraded to...
pyrimidines are degraded to... |
purine -> uric acid
pyrimidines -> malonyl-coa methylmalonyl coa (which are used in fatty acid biosynthesis and the TCA) |
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|
wha tis the purpose of hypoxanthine guanine phosphoribosyl transferase (HGPRT)
|
uses hypoxanthine from food to be directly incorporated into PRPP using hypoxanthine guanine phosphoribosyl transferase
Hypoxanthine -> IMP |
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|
lesch-hyan syndrome deficient enzyme and symptoms...
|
defect in HGPRT
* motor ysfunction, self destructive behavior *causes uric acid accumulation (babies show up in ER with blood and gritty/sandy deposits in diaper, uric acid crystals cut tissues) bbuildup of hypoxanthine goes to uric acid instead of salvage pathway |
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|
What are the major divisions of the cell cycle:
|
-G0 (gap 0) is not technically a division of the cell cycle, but a resting state prior to entering the cell cycle
Interphase - everything else -G1 (gap 1) - Cell expands in mass, where cells enter or exit the cell cycle -S phase - DNA is replicated -G2 (gap 2) - syntheiss (esp microtubules) -Mitosis - Interphase, prophase, metaphase,anaphase,telophase,cytokinesis |
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what does cyclin do
|
binds and activates a cyclin-dependent kinase (CDK) and these two together control the cell cycle
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what does APC do
|
anaphase promoting complex (PAC) is an E3 ubiquitin ligase which targets the cyclin
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|
how many cyclins and cdks are there in humans?
|
4 cyclins and 4 cdks -- one for each stage of the cell cycle
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|
name and describe the functions of the different cyclins
|
Cyclin D: CDK6/CDK 4 -> get cell through G1
Cyclin E: CDK2 -> Get cell from G1 to S Cyclin A: CDK2 ->Drives cell through S phase and G2 phase, into M phase Cyclin B: CDK1 -> Get cell through mitosis |
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What are the 3 major checkpoints
|
1. G1 fxns at transition of G1 to S phase
Asks, Is cell big enough? Are growth signals present? Are there enough nutrients? 2. Multiple DNA damage and DNA replication checkpoints Make sure DNA isn’t damaged and has replicated before move forward 3. Spindle checkpoint Don’t want to pull chromosomes apart before spindle is built and chromoso |
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if you add caffeine to a cell...
if you ad hydroxyurea to a cell.. if you add both to a cell... |
Caffeine inhibits the DNA replication checkpoint
Hydroxyurea blocks replication (ie causes damage) |
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|
Describe G1-S checkpoint regulation
|
responds to enviornmental conditions by controlling transcription of cyclin E which needs to drive from G1 to S
release of Rb (retinoblastoma) inhibition of E2F protein * Rb normally binds and inactivates E2F. When growth signals make G1-Cdk active, Rb gets phosphorylated and releases E2F. E2F is now active and acts as a transcription factor. |
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|
retinoblastoma...
|
* Common childhood cancer of the eye which comes in sporadic and hereditary forms.
• The hereditary form is due to mutation in Rb gene. • Somatic cells are heterozygous for the mutation and tumor cells are homozygous. • Rb is therefore a tumor suppressor gene, because its presence prevents tumor. Mutations in Rb are what lead to Retinoblastoma |
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|
Describe regulation of the DNA Damage Checkpoint
|
• Damage in G1 or early S acts through control of cyclin-cdk activity
• p53 and CDK inhibitor p21 are key players • p53 a transcription factor, is ordinarily is synthesized constantly, but normally degraded by Mdm2 (an E3 ligase) • If DNA damage is present, there is protein kinase that phosphorylates p53 so that it is no longer recognized by Mdm2 • p53 then moves to the nucleus and turns on transcription of genes, such as p21 which is a cdk-inhibitor • This mainly affects cyclin A and cyclin E |
|
|
Li-fraumeni syndrome
|
• Inherited p53 defect is called Li-Fraumeni syndrome, which leads to many types of cancers
• Very rare, because you get a pattern of earlier onset of cancer so that eventually nobody lives long enough to inherit disease |
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|
weel kinase...
|
damage in late s or g2 uses weel kinase which phosphorylates cdk to inactivate it, works on cyclin A or cyclin B
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|
describe the regulation fo the spindle checkpoint
|
Rb is involved in the signal to start the cell cycle
• p53 is involved in DNA damage early in the cell cycle • Kinase Wee1 is involved in DNA damage later in the cell cycle • BubR1 is involved in the spindle checkpoin |
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|
What are the roles of the carbons on the ribose sugar in DNA/RNA
|
(start nubmering from the site after the oxygen)
C1 - base attachement C2 - determining site of DNA v.s. RNA (H v.s. OH) C3 - attachment of phosphate C4 - branch in ribofuranose C5 - attachment of phosphate |
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|
what is on the final 5' end of and of 3' end of DNA? wwhat is the order of conventional reading?
|
the 5' end usually has a phosphate, the 3' end usually has a free OH group.
conventional readign : 5' to 3' |
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|
Draw the purines and pyrimidines
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|
Adenine will form ___ bonds with ____
Guanine will form ___ bonds with ____ |
Adenine will form 2 hydrogen bonds ith Thymine
Guanine will form 2 hydrogen bonds ith Cytosine |
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|
DNA is read in which direction
DNA is assembled in which direction |
written: 5 to 3
template strand read: 3 to 5 new strand synthesized from 5 to 3 |
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|
describe assembly of the primer strand in terms of the phosphates
|
All nucleosides have 3 phosphates, the first remains with the primer strand and the other two leave as phyrophosphate (energy from the hydrolysis of these phosphates is used for further DNA chain growth)
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|
what is the rate of dna replication error, how does it occur most frequently and how is it corrected?
|
DNA replication occurs once every 1E8 base pairs (only about 2 times in the largest chromosome (#1)) due to tuotmers of normal bases, it is corrected by monitoring the regulation of hydrogen bonds of the two strands. the incorrect base swings out to the editing site of DNA polymerase
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|
what is the rate of dna replication error, how does it occur most frequently and how is it corrected?
|
DNA replication occurs once every 1E8 base pairs (only about 2 times in the largest chromosome (#1)) due to tuotmers of normal bases, it is corrected by monitoring the regulation of hydrogen bonds of the two strands. the incorrect base swings out to the editing site of DNA polymerase
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|
which protein starts DNA replication...
|
Cyclin A-CDK2 will phosphorylate proteins bound at replication forx thus activating them and tirggering the start of replication
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|
Why do you need DNA primase and not just DNA polymerase in the opposite direction
|
* DNA polymerase needs a free 3' OH on which to attach a nucleotide
* DNA Primase creates a short RNA primer |
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|
Sliding Clamp and clamp loader
|
Sliding Clamp: keeps DNA Polymerase on the string to allow for long streches of DNA
Clamp Loader: is required to get the clamp onto the DNA, the clamp loader attaches two halves of a sliding clamp to make a donut-shaped molecule around the RNA primer at its 3' end |
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|
what are the three types of phospholipase classes and where do they cleave
|
PLAs cleave ester bonds and produce lysophospholipids and fatty acids
PLCs cleave phosphoester bonds and produce diacylglycerol (DAG) and inositol triphosphate (IP3) PLDs produce phosphatidic acid |
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|
what causes the bilayer to self-assemble in H2O
|
the hydrophobic effect
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|
why do phospholipds have two tails instead of one..
|
geometry - maintains cylinder shape because of two tails, if only noe tail -cone shape - called a lysophospholipid
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|
why don't lipids have shorter tails, why not longer
|
need to e long enough to have enough hydrophobic energy, why not longer: van der waals forces make packing too tight - membrane would freeze
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|
why does the 2nd phospholipid tail typically have double bonds
|
fluid molecule - still fluid at low temperatures
|
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|
what purpose does cholesterol serve in the bilayer
|
increases mechanical and chemical stability of bilayer
makes it more viscous, prevents cell from freezing increases resistance to tearing may help form rafts - areas of the membrane rich in cholesterol and sphingomyelin |
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|
Where are different phospholipids found in the different locatinos on the membrane..
|
--Phosphatidylcholine (PC)
--Phosphatidylethanolamine (PE) --Phosphatidylserine (PS) - a marker for apoptosis --Sphingomyelin (SM) **sugars are usually found on the outside |
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|
What are three major DNA repair mechanisms
|
1) Direct repair (photoreactivation) - utilized in therepair of thymine dimers using a photolyase enzyme (recognizes a kink caused by thymine dimer, binds to it then using N5,10 THF cofactor, absorbs light and uses that photon energy to break the thymine dimer bond
2) Base Excision Repair - An enzyme simply removes the damaged base; used for repairing deaminated bases and abasic sites 3)Nucleotide Excision Repair - Enzyme finds damaged base, removes a chunk, and replaces the sequence |
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|
Describe the steps of base excision repair:
|
1) uracil DNA Glycosylase scans DNA looking for uracil, cuts the base out, and creates an abasic site
2) AP Endonuclease finds abasic sites, breaks the phosphate backbone on both sides and removes the sugar phosphate of the previously removed base 3)DNA polymerase will add in a new nucleotide to replace the cleaved out one. 4)DNA Ligase will seal the gaps fully incorporating newly added base. |
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|
Describe the process of nucleotide excision repair:
|
1) Large multienzyme complex sans DNA looking for distortions of
double helix. 2) Nuclease makes nicks upstream and downstream of lesion or dimer. 3) DNA Helicase will unwind the DNA separating out the nicked portion from the correct coding portion 4) DNA polymerase will fill in the large gap created by the removal of the sequence. 5) DNA ligase will seal the nicks. |
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|
What are the functions of the different DNA Polymerases
|
|
|
|
How does double strand breakage occur and how is it repaired
|
*occurs by mutagens (and can lead to translocations)
1) Nonhomologus end joining-the process of reattaching two ends together, even though some nucleotides were lost due to degradation from the ends ; leads to a loss of info and thus a mutation 2) Homologus end joining - the prefered method which restores teh lost nucleotides by looking at homologus chromosome |
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|
Describe the process of double-strand breakage repair (homologous end-joining)
|
1) Chromosome has a
double strand break. 2) Exonuclease creates two protruding 3’ single stranded ends chewing up the 5’ end. 3) The homologous chromosome is brought in to act as a template for the lost bases. 4) Each of the 3’ends of the broken DNA find homologous region in the maternal chromosome 5) The DNA complex is then segregated back into separate chromosomes by selective strand cuts. |
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|
how do translocations occur
|
occur with a double-strand break during meiosis crossing over process
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|
what makes up the chromosomes
|
chromsomes = chromatin is composed of DNA + proteins
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|
where are chromosomes condensed and dispersed
|
condensed during mitosis, dispersed during interphase
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|
what is the makepup of DNA (in terms of "useful" dna)
|
20% of the material are genese, 2% of total genome is protein coding (because of the existence of regulatory sequences, promoter introns)
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|
which part of the gene encodes proteins
|
the exon part (EXon is EXpressed)
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|
|
name the sources of dna damage
|
Oxidation, Hydrolysis, Methylation
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|
Which is the most common deamination of a DNA base
|
: Cytosine -> Uracil
|
|
|
Describe the Acetylcholine/NO pathway
|
Acetylcholine release by nerve terminals in the blood vessel wall activates-> activation of NO synthase in endothelial cells lining the blood vessel -> cause them to synthesize NO -> No diffuses out of the cells and into the underlying smooth muscle cells -> here it activates guanylyl cyclase to make cGMP -> cGMP triggers a response that causes the smooth muscle cells to relax/dialate, enhancing blood flow
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|
what are the two types of signaling molecules
|
1. Hydrophilic: These cannot cross the plasma membrane (hydrophobic lipid bilayer) directly
and therefore bind to cell surface receptors, which in turn generate intracellular signals. 2. Hydrophobic: Small hydrophobic signaling molecules that can diffuse across the plasma membrane bind to intracellular receptors that are present in either the cytoplasm or the nucleus of the cell. |
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|
List and describe the different examples of cellular signaling:
|
1) contact dependent signaling - requires the cells to be in direct contact. One cell has the signal molecule and one has the receptor EX: T-Cell activation via peptides on the surface of an antigen-presenting cell
2)Paracrine signaling: Secreted signaling molecules affect cells in the local/immediate environment; local signaling; rapid;degraded quickly; turn over quickly;short half-life 3. Synaptic Signaling: occurs in nerve cells; action potentil through the axon of a neuron; release of neurotransmitters into synapse; fast and precise; short lived as ligand molecules are degraded rapidly 4)Endocrine Signaling: involves a hormone secreting cell which releases hormone in the blood; can strech ofver long distances; slow repsonse time; 5)autocrine Signaling: A cell secretes signaling molecules that bind to own receptors; strong with group of cells 6)Gap junctions: communication with neighbors via gap junctions; cells share small molecules |
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|
ErbB receptors are..
|
ErbB 1,2,3,4 Dimerize with same type of ridfferent type,Complicates intracellular pathways, get many
more different signals because bind to selective heterodimers. |
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|
what is the role of NO
|
plays an important role in smooth muscle relaxation in blood vessel walls (blood vessel dilation). Can diffuse across plasma membranes
|
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|
what is the nuclear receptor super family
|
small hydrophobic signaling molecules that bind to nuclear receptors. these nuclear receptors then bind to DNA directly and activate or repress the transcription of target genese (cortisol, estradiol, testosterone, vitamin D3, thyroxine, retinoic acid)
|
|
|
what is the difference between primary-response genes and secondary-response genes
|
steroid hormones bind to specific receptors; binding creates steroid-hormone-receptor cmplex that activates transcription of primary-response genese by unmasking; these genes code for proteinst that comprise the primary response signal pathway; some primary-response proteins then shut off transcription of the primary-response genes, others turn on transcription of the secondary-response gense which code for secondary-response proteins which are used by the cell to respond to the orgiginal hormone signal
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|
|
describe the intracellular signaling mechanisms
|
* extracellular sinal molecule binds to the cell surface receptor
* signal then travels from the cell surface to the cell nucleus via different kinds of intracellular proteins in a signaling pathway |
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|
what are GCPRs and describe their structure
|
G-protein coupled receptors
* 7 transmembrane structure (serpentine receptor) *extracellular portion contains the ligand-binding domain when bound causes conformational change allowing it to bind to the G-protein |
|
|
describe the structure of G-proteins
|
* attached to the cytoplasmic face of the membrane
*consist of three subunits- alpha,beta,gamma *alpha binds to GTP or GDP *alpha and gamma have lipid modification that anchor them to the membrane *when GTP is bound will undergo confirmational change allowign it to interact with effectors *in GDP-bound state -> inactive *Gs (stimulatory) and Gi(inhibitory) are the two major families of G-protins and are repsonsible for stim or inhib of adenylyl cyclase *alpha is usually the catalytic site |
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|
diagram the molecular events that take place during the activation cycle of a G-protein coupled receptor
|
*GDP-bound in inactive state
*signal molecule binds to the extracellular ligand bindign domain, causing a conformational change (also to the alpha subunit) alpha releases GDP and binds GTP to become active form capable of binding effectors *GTP binding causes dissociation fo beta-gamma complex * receptor stays active while the external signal molecule is bound so can amplify |
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|
How does the inactivaton of G-protein occur
|
*GTPase activity of the alpha subunit hydrolyzes GTP back to GDP and then reassociates with the beta-gamma complex to reform the inactive G-protein
|
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|
what is the role of adenylate cyclase in G protein signaling
|
cAMP is synthesized by adenylate cyclase which is a membrane bound enzyme activated by G-proteins Galpha proteins actiavate adenylate cyclase which then conversts ATP into cAMP degradation of cAMP into 5'-AMP is catalyzed by cAMP phosphodiesterase
|
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|
what is the role of PKA in the g-protein pathway
|
Once cAMP is synthesized by adenylate cyclase it produces its effects in the cell through the
activation of PKA (Protein Kinase A aka cAMP-dependent protein kinase).PKA exists as a tetramer, containing 2 regulatory subunits and 2 catalytic subunits. The regulatory subunits inhibit the catalytic subunits. cAMP binds to the regulatory subunits and causes a conformational change resulting in their dissociation from the catalytic subunits, which are then free to phosphorylate effector molecules. |
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|
Describe the process by which cAMP activates the cAMP-dependent protein kinase, leading to glycogen breakdown in skeletal muscle cells.
|
In skeletal muscles, epinephrine binds to the GPCR, resulting in the activation of Gs and
subsequently adenylate cyclase. The increase in cAMP concentration due to the action of activated adenylate cyclase is responsible for activating PKA. PKA phosphorylates phosphorylase kinase, which then phosphorylates and activates glycogen phosphorylase (remember two types A and B, depending on what type of tissue – liver or muscle), the enzyme responsible for the degradation of glycogen into glucose. PKA also phosphorylates glycogen synthase, resulting in the inactivation of the enzyme that catalyzes glycogen synthesis. The breakdown of glycogen in skeletal muscles is enhanced by PKA’s activation of the enzyme needed to promote glycogen breakdown and the simultaneous inactivation of the enzyme that promotes glycogen synthesis. Normally the action of PKA in the cell is inhibited by PP1, but PKA phosphorylates a phosphatase inhibitor protein for PP1. This PP1 inhibitor complexes with PP1 and sequesters it so it is no longer able to inhibit the cAMP-stimulated phosphorylation reactions within the cell. |
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|
Discuss how cAMP triggers the increased transcription of genes containing cAMP
response elements. |
Cyclic AMP is also involved in the transcription of genes. The increased concentration of cAMP
due to the activation of GPCRs results in activation of PKA. As mentioned before, activated PKA divides into its catalytic and regulatory subunits; in this case, the catalytic subunits enter the nucleus through nuclear pores and phosphorylate CREB (a transcription element binding protein), thereby activating it. CREB now recruits the co-activator CBP (CREB-binding protein) and the CREB-CBP complex interacts with the DNA at the CREB-binding element (also known as a cAMP response element, CRE) to promote gene transcription. Only transcription of genes that contain an upstream CRE are influenced by this pathway. It takes longer to see the effects of transcription (minutes to hours) than to see the effects of second messengers (seconds) (e.g. activation of glycogen metabolism). |
|
|
describe the activation of PLC-beta
|
|
|
|
what are the two broad classes of tyrosine kinases
|
receptor-type TK (epidermal growth factor receptor/insulin receptor)
Non-receptor tyrosine kinases such as v-src and c-src |
|
|
How are Nuclear Receptors activated?
|
inactive receptor contains ligand-binding domain, DNA-binding domain, and inhibitory protein; when ligand binds to receptors receptor undergoes conformation change, loses its association with the inhibitory protein and binds to a co-activation protein, DNA-binding site becomes unmasked
|
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|
list and describe the three types of cell surface receptors
|
1) ion-channel linked receptors: these allow rapid synaptic signaling between electrically active cells, signals bind to receptors causing conformation change that opens the channle allowing the ions to flow through it
2) G-protein linked receptors: act indirectly to change activity of target cells via relay protein (G-Protein) that regulations the activity of another membrane bown receptor (G-protein coupled receptor-> g-protein-> effector); 3)enzyme linked receptors: the enzyme portion of the recptor is interacellular. binding of ligand to the receptor increases the catalytic activity of the interacellular domain of receptor |
|
|
what is the cholera and pertussis mode of action..
|
ADP-ribosylates Gs makign the alpha subunit unable to hydrolyze GTP and leaves the protein locked in an active state resulting in continuous activation of adenylate cyclase and consequently a hight production of cAMP in the intestinal epithelia
*pertussis toxin (whooping cough) ADP-ribosylates Gi making it unable to interact with its effectors and thus remain GDP0bound which causes an increase in cAMP production |
|
|
what are three mechanisms for desensitization of a g-protein coupled receptor
|
1. receptor inactivation - modified so it doesn't bind the ligand
2. Receptors may become internalized via clathrin-coated bpits so that they care nto accessible to the ligand 3. Recptors are destroyed in the lysosome and there is a decrease in receptor synthesis..receptor down-regulation |
|
|
which PLC isoforms are activated by which proteins
|
Gq -> PLC-beta
Ca++ -> PLC-delta1/PLC-epsilon phosphorylated tyrosines -> PLC-gamma1 |
|
|
what are three differences in the modification of heterochromatin v.s euchromatin
|
acetylation - euchromatin is usally acetylated, heterochromatin is not, (is methylated on Lys9) which causes HP1 to bind and helps pack
positional effects - the spreading |
|
|
wha tis the mechanism of dna silencing..
|
5-methylcytosine, modification of DNA helps determine whether it is expressed,and 5-methylcytosine silences specific areas
* DNA methytransferase (MT) takes methyl groups from SAM to methylate cytosine residues in promoter reginos - CPG islands (CG rich regions of DNA which trigger gene silencing *Methyl CpG Binding Proteins (MeCP2) recognize and bind to 5-methylcytosine groups MeCP2 recruits histone deacetylases (HDAC) to additionaly modify histone tails leading to heterochromatin formation, deacetylate -> turn off |
|
|
what don't females usually express x-lilnked traits
|
female cells are chimeric, resulting from the inactivation of one of the x-chromosomes along it's cellular lineage which may not have mutated gene, but the trait is less likely to be expressed
|
|
|
what are the two types of chromatin and what are their differences?
|
hetero - "different", eu - "good"
1.) Heterochromatin a.) Highly condensed, even in interphase b.) Transcriptionally inactive c.) Replicates late in S-phase 2.) Euchromatin a.) Organized in 30-nm fibers during interphase b.) Transcriptionally active c.) Replicates early in S-phase |
|
|
wilm's tumor
|
7% of all childhood cancers, kidney tumor
*defect in imprinting of IGF2 (insulin-like growth factor 2) gene, usually IGF2 expressed in paternal locus but instead is imprinted in maternal locus, causes expression of maternal locus and both copies are active- 2x stimulatory signal, doubling of growth factors are produced, leading to cancer |
|
|
hetrochromatin/euchromatin which are light/dark bands
|
hetrochromatin are the dark (more densely packed?) and euchromatin are the light
|
|
|
basis of these diseases: Wilms Tumour, Rett Syndrome
|
a.) Rett Syndrome
• Mutation in gene encoding MeCP2 • Can still methylate DNA, but cannot recruit other proteins to condense whole chromatin • X-linked neurodegenerative disorder • Only observed in females because it is fatal to men in utero, since they only receive one X chromosome • 1:10,000-15,000 • Affected females have one good copy and one bad copy of gene, but if enough of the bad copies are shut down during X-inactivation, the patient can live on b.) ICF Syndrome • Rare loss of DNA Methyltransferase 3-B • More severe than Rett’s Syndrome • Immunodeficiency, Craniofacial abnormalities |
|
|
describe bubr1 regulation pathway in the kinetochores control of the spindle checkpoint
|
bubr1 is active if microtubles are nto attached to the kinetochore and activates mad2p which in turn inactivates APC preventing the start of anaphase; when microt attach bubr1 is inactivates which inactivates mad2p allowing APC to trigger anaphase
|
|
|
what is condensin -
|
a large protein that drives the condensation of mitotic chromosmoes
* ahve an ATPase at their heads work in a sissor-like manner condensing chromatin |
|
|
what are cohesins
|
holds siter chromatids together, is similar in composition to condensins
*APC is an E3 ubiquitin ligase that indirectly regulates the degradation of cohesins as long as cohesins are present on the chromosome the sider chromatids cannot separate (therefore no transition from metaphase to anaphase) |
|
|
what is securin
|
securin separates from the protein separase, which causes the degradation of the cohesin subunit scc1 allowing the chromatids to pull apart
|
|
|
telomers consist of
|
G rich regions (TTAGGG)n in humans
* can be 5-15 kb long |
|
|
describe the "end replication problem"
|
*After replication is complete the RNA primers from the leading and lagging strands are removed and replcated with DNA by α-DNA polymerase
*the primer on the lagging strand opposite the 3' end of the template is removed but cannot be replaced by DNA polymerase because there is not a 3' OH available as a primer. This results in an overhanging edge and loss of inormation from opposite ends of both strands |
|
|
Describe the three most common ways signal can be promoted by the recruitment of SH2 containing proteins...
|
1)PI3-kinase -- PI3K is recruited to the membrane by virtue of its SH2 domains docking onto a RTK, it's substrate PIP2 generates PIP3 which recruits PKB and PDK1 to PIP3 which activates them protecting the cell form apoptosis
2) PI3-kinase -- when the SH2 sites on Pi-3 kinase bind a conformational change occurs and the catytic activity of p110 becomes activated PLc-gamma -- PLC-gamma is recruited to RTK the RTK phosphorylates and activates PLC-gamma which cleaves its substrate (a membrane phospholipid) to promote signaling |
|
|
what are adaptor proteins
|
another class of proteins which are recruited to RTKs
* have no enzymatic function, act as glue to bring together two other proteins * Grb2 bbinds to a protein called son of sevenless (SOS) which is a guanine nucleotide exchange factor (GEF), which is specifice for the small g-protein called ras *ras cycles between active GTP bound state and inactive GDP bound state |
|
|
describe the MAP kinase cascade
|
active Ras protein (recruited fromt he adaptor proteins) triggers a cascade of Ser/Thr phosphorylations (MAPKKK--map kinase-kinase-kinase-- MAPKK, MAPK ) which end up changing the activity of gene regulatory proteins
*when activated MAPKs can dimerize and tranlocate to the nucleus where they have a number of targest *the mapks specifically phosphorylate gene regulatory proteins, the major one of which is elk1 (controls transcription of early genes) |
|
|
describe the structureof tyrosine kinases
|
*an N-terminal to bind ATP and a C-terminus to bind substrate
*a single hydrophobic transmembrane alpha-helix attaches the receptor to the membrane (about 25) amino acids or so * the helix passes through the membrane only once *diverse extracellular domains with ligand-binding sites *mostly monomeric except for insulin receptor (a2b2 structure) |
|
|
when active, the RTK is...
|
dimerized (when monomeric is unactivated)
|
|
|
autophosphorylation happens when...
|
one molecule in the dimer phosphorylates the other, so it is intermolecular or trans phosphorylation
|
|
|
combinatorial signaling
|
different combinations can signal differently such as the case with heterodimers
|
|
|
what are the three different pathways for cell death
|
autophagy associated cell death
apoptosis necrosis |
|
|
what are the four pages of apoptosis
|
1. death signals (intrinsic: cytochrome c is released from the cell during apoptosis by mitochondira and extrinsic: death signals that interact with receptor sites and lead to clustering of capsases
2. integration of control stage 3. execution phase 4. removal of dead cells by pagocytosis |
|
|
What are the steps of RNA synthesis
|
1. Binding of TBP to the TATA box
2. TFIIA is recruited by TFIID 3. Binding of TFIIB follows 4. Binding of TFIIF 5. RNA pol II binds, follwed by TFIIE Binding of TFIIH, whose helicase activity unwinds the DNA template Basal transcription apparatus is assembled |
|
|
What is sir2?
|
an NAD-dependent histone deacetylase that is responsible for the formation of
heterochromatin in yeast and localizes to telomeres |
|
|
how is rna synthesis initiated:
|
The RNA polymerase slides along the DNA template. The
sigma factor of the holoenzyme recognizes and binds to the promoter sequence to initiate transcription – when the sigma factor is bound this is known as the closed promoter complex. The RNA polymerase has helicase activity to unwind the DNA by breaking the H-bonds about 17 base pairs at a time. Once the DNA is unwound by RNA polymerase, it is called the open promoter complex and can start adding nucleotides |
|
|
what do the different rna pol do
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rna pol i : nucleolus - ribosomal RNA
rna pol ii: nucleoplasm - all protein-coding genes, snoRNA, snRNA and micro RNA rna pol iii: nucleoplasm - trna |
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how is mrna synthesis regulated
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phosphorylation of rna pol II by thiih releases the pol ii from TFs and allow elongation of the RNA chain
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name 4 inhibitors of transcription
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rifampicin - blocks RNA-DNA hybrid generation (prokaryotic)
actinomycin D - intercalcate between DNA base pairs (eukaryotic/prokaryotic) -streptolidigin - binds to bacteral RNA polymerase and prevents phosphodiester bond formation ( prokayrotes) -a-amanitin - inhibits eukaryotic rna pol |
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what are the different methods of transcription regulation
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* competitive DNA binding -
* masking the activation service - * direct interaction with the general transcription factor * recruitment of repressive chromatin remodeling complexes * recruitment of histone deacetylases |
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what does thyroxine do
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increaes cellular metabolic activity
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what does cortisol do
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effects the metabillism of proteins, carbohydrates and lipids and suppresses inflammatory reactions
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what does progesterone do
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prepares the uterus for preganancy and maintaines the preganancy and stimulates the development of the alveolar system in mammary glands
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what does estradiol do
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stimulates the development and maintenance of female sex characteristics
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what does testosterone do
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stimulates the development and maintenance of mail sex characteristics
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what does vitamin d do
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stimulates calcium intake and retention
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what do retinoids do
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stimulate vertebrate development
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How does is the 5' cap added
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this happens cotransscriptionally, while the transcript is being made, first a phosphate is removed from the 5' end of the nascent mRNA transcript by hydrolysis. The the remaning 5' diphosphate forms a phosphodisester bond with a GTP, Finally a methy group is transferred from S-adenosylmethionin to the N-7 nitrogen of base guanine
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describe the process of Group 1 mRNA splicing
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1. The hydroxyl of guanosine attacks the phosphodiester bond between the upstream exon
and the intron, forming a new phosphodiester bond. 2. 2. Part of the intron holds the upstream exon in place to allow the OH of the 3’ end of the upstream exon to attack the phosphodiester bond between the intron and the downstream exon. 3. This second reaction breaks the junction of intron and the downstream exon and brings the two exons together. The intron sequence of this type of self-splicing is conserved. This is necessary because the exact conformation is necessary to hold the intron and two exons in close proximity.] |
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describe group II mRNA self-splicing and how is it different from Splicesome-catlyzed splicing of mRNA
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2' OH of adenosine attacks the P-bond in 5' splice site
-3' OH end of the upstream exon attacks the P-bond of the 3' splice site -P-bond between upstream exon and downstream exon si formed relasing lariat Different becasue group II is found in fungal mitochondria, plant chlorplasts and a wide varite of bacteria, Splicesome requires snRNAs which bind to pre-mRNA to form large complexes |
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describe the spliceasome assembly
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1. U1 snRNP binds to the 5’ splice site
through specific base pairing (it has a complementary sequence) 2. U2 snRNP binds to the branch site (it has a complementary sequence) 3. U6 snRNP is complementary to part of U2 snRNP 4. U5 snRNP binds to the 5’ splice site 5. U4 snRNP then binds to form the complete spliceosome. a. The binding of U4-U5-U6 complex requires ATP hydrolysis |
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what are the modifications of trna before it is exported from the cell
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- cleavage of 5' leader sequence by RNase P
- removal of intron by splicing - replacing 3' UU with CCA - base modification |
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whater the the thre ways that mRNA precursors are processed
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-addition of cap to 5' end
-addition of poly A tail to 3' end -removal fo introns by splicing |
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the 5' cap of the pre-mRNA is important to
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A. Stabilize the mRNA by protecting their 5’ end from
nucleases and phosphatases B. Export the mRNA out of the nucleus C. Enhance the translation of the mRNA |
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What are the 3 different types of RNA splicing
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1) Group 1 splicing
2) Group 2 splicing 3) splicsome-catalyzed splicing of mRNA |
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what are alternative poly a adenylation sites and rna editing
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- alternative sites usually aauaa causes different termination sites for a given gene, b-lymphocytes will have a membrane bound antibody or secreted depending on where the rna is cleaved
-rna can be edited by using cytosine deaminase to deaminate the cytosine in the CAA sequene turning it into a uridine UAA is a stop codon which causes, for example, B-100 to become B-48 |
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what are the following codons: AUG, UAA, UAG, UGA
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AUG - stop
UAA, UAG, UGA - stop |
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name the key features of a tRNA molecule
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There are four areas where the bases are
actually paired to each other (see the dotted lines), giving you double stranded regions of RNA. • The 3’ end (on top) is where the amino acid would be attached. The 3’ end always terminates with CCA. • On the bottom, you see the anticodon, which actually reads the mRNA triplet. This is the most variable part of the tRNA molecule. In addition to the anticodon loop, you have two others: (1) the TψC loop, which is rich in pseudouridine bases (the symbol for pseudouridine is ψ), and (2) the DHU loop, which is rich in dihydrouridine bases. |
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how are tRNA molecules activated
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the tRNA molecule must be activated (it must be covalently coupled to an amino acid). The enzyme responsible for this task is the aminio-acyl tRNA synthetase. First a high energy bond must be produced between the aminio acid and AMP. In the next step, the aminio acid is addd to the tRNA and AMP is released. Thus, the activated tRNA molecule- the aminioacyl tRNA - is produced. When the aminio acid binds, it des so to the sugar, either to its 3' hydroxyl group or to its 2' hydroxyl group
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what does pepidyl tRNA do
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attaches to the C-TERMINUS of the growing polypeptide, the amino-acyl tRNA that adds to the elongating chain now is called the peptidyl tRNA
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describe the process of tRNA binding and protein elongation during translation
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In this diagram we first see a peptidyl tRNA molecule on the P site of the ribosome. Notice that
there is only one amino acid in the tunnel. An aminoacyl-tRNA molecule joins in and goes to the A site. A peptide bond is formed between the amino acid on the peptidyl tRNA molecule and that of the aminoacyl-tRNA molecule. Now, there is a shift: the former aminoacyl-tRNA molecule assumes the P site. It is now the new peptidyl tRNA. The former peptidyl moves on to the E site. |
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describe the steps of Eukaryotic initiation
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1. eIF4E recognizes the 7-Met-G cap. It binds to the mRNA transcript at the cap.
2. eIF-2(GTP) is bound to Met-tRNA and the 40S ribosomal subunit 3. eIF4G binds to both eIF4E and 40S and brings the initiator complex to the messenger start site. 4. In an ATP dependent way, the complex with eIF-2 begins to translocate along the message until it finds the first AUG codon. Moves from 5’ to 3’ direction along the message scanning for the first AUG. 5. If there is a second AUG along the line, initiation machinery never gets there (note: this is generally true, but there are exceptions to the 1st-AUG rule. For example, if the first AUG is not surrounded by the appropriate context (e.g lacks a Kozak sequence) the ribosome may skip this AUG and proceed to a downstream AUG that is in the appropriate context. The mouse mu-Opioid receptor, for instance, has three AUG’s upstream of the main AUG that codes the first a.a. of the mu-Opiod receptor protein. The upstream AUG’s appear to have a regulatory function, inhibiting the rate of mu-Opioid receptor translation.) 6. The complex finds the AUG, eIF-2(GTP) is hydrolyzed to GDP, allowing for the large subunit to come in and bind |
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describe how control of translation by eIF2 phosphorylation occurs
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1. Nutrients are low → protein kinases activated.
2. Protein kinases phosphorylate eIF-2(GDP). 3. eIF-2B binds to eIF-2(GDP) → the complex is stabilized and inactive. 4. Because there is more eIF-2(GDP) than eIF-2B in a cell, eventually all the eIF-2B is sequestered and eIF-2(GDP) cannot be recycled. 5. Translation is turned off. |
