Biochem II Exam #1

Question 1

What are examples of first messenger and their responses?

Answer 1

Acetylcholine- muscle contraction

Epidermal growth factor-cell proliferation

Epinephrine- increased pulse rate; degradation

Glucagon-glycogen degradation

Insulin-Glucose uptake

Ions and small molecules-membrane depolarization; intracellular signaling; gene expression

Question 2

Second messenger examples

Answer 2

cAMP
cGMP
DAG
IP3
Ca

Question 3

Consequence of Phosphoinositide Cascade

Answer 3

*receptor mediated activation of PLC leads to an increase in IP3 and DAG levels

*DAG binds to and stimulates the activity of PKC, which phosphorylates target proteins

*IP3 activates Ca channels on the ER and causes an increase in cytoplasmic Ca; goes to PKC or to calmodulin
The activities of PKC and calmodulin are both regulated by Ca binding

Question 4

Classes of receptor proteins in Eukaryotes

Answer 4

*G protein-coupled receptors- dissociation of heterotrimeric G protein complex; activation of adenylate cyclase and PLC

*Receptor tyrosine kinases- Phosphorylates Tyr residues in target proteins to create docking sites for intracellular signaling

*Tumor necrosis factor receptors-transmit extracellular signals by forming receptor trimers; controls inflammation and apoptosis

*Nuclear receptors-modulate gene expression through protein-DNA and protein-protein interactions; only one that is not transmembrane

*Ligand-gated ion channels-control flow of K+, Na+ and Ca ions across the cell membrane in response to ligand binding.

Question 5

GPCR signal transduction systems

Answer 5

G alpha- G protein subunit with GTPase activity

Gaby-complex of Ga, Gb, and Gy subunits associated with GPCRs.

GAP-protein that stimulates GTPase activity of the G protein to inhibit signaling

GEF-Protein that promotes GDP-GTP exchange to activate signaling

PKA-cAMP dependent enzyme with kinase activity

PKC-lipid activated enzyme with kinase activity

RGS- GTPase activating protein that is associated with GPCRs

Question 6

Shared or parallel GPCR-mediated signaling pathways

Answer 6

Glucagon and B2 adrenergic receptors activate a SHARED cAMP-mediated signaling through Gs, which stimulates AC

a1-adrenergic receptors activates PARALLEL pathways using Gs and Gq
*the Gq pathway stimulates PLC activity, leading to production of DAG and IP3

**all 3 of these signaling pathways converge on target proteins in liver cells that degrade glycogen, leading to increased rates of glucose export.

Question 7

Activation of PKA by cAMP

Answer 7

Activation of PKA by cAMP requires the dissociation of regulatory subunits and catalytic subunits

4cAMP molecules bind to the inactive R2C2 complex and induce a conformational change in the regulator subunit that results in the release of 2 catalytically active monomers.

Question 8

MAP Kinase signaling pathway

Answer 8

*activated RAS protein stimulates the mitogen-activated protein kinase Pathway, which initiates a phosphorylation cascade consisting of 3 MAP proteins
-Raf, MEK, and ERK

*the cellular response to activation of the MAP kinase signaling pathway is regulation of gene expression and increased rates of cell division.

Question 9

Oncogenic Ras mutations cause chronic stimulation of MAP kinase signaling pathway

Answer 9

The most common oncogenic Ras mutations lead to defects in the Intrinsic GTPase activation and thereby block Ras protein inactivation.

Dominant Ras mutations in the GTPase domain lead to chronic stimulation of the MAP kinase signaling pathway, even in the absence of growth factors.

Question 10

Insulin signaling pathway

Answer 10

controls 2 major downstream pathways
1. MAP Kinase
2. P1-3K

*Insulin receptor tyrosine phosphorylation of IRS and Shc proteins, these bind to the receptor cytoplasmic domain through PTB.

*this leads to the stimulation of 2 downstream signaling pwathways
1. phosphorylates Shc binds to GRB2, whcih activates the MAP kinase pathway, which leads to altered gene expression and cell divsion.

2. phosphorylated IRS binds to PI-3K and activates a downstream signaling pathway that leads to increased glucose uptake and stimulation of glycogen synthesis.

Question 11

PIP3 Activation and Insulin signaling

Answer 11

Insulin receptor signaling activates P1-3K through IRS, which leads to the production of PIP3.

*Phosphorylation and activation of Akt by PDK1 initiates a downstream signaling pathway in liver cells that stimulate glucose uptake and glycogen synthesis

Question 12

TNF- receptors signal through cytosolic adaptor complexes

Answer 12

Activation of trimeric TNF receptor complexes by TNF-alpha binding induces a conformational change that promotes exchange of SODD to TRADD

Adaptor complex assembly on the cytoplasmic tails of TNF recptors is mediated by DD, which function as protein- protein interaction modules.

Question 13

Proteolytic pathway-programmed cell death

Answer 13

1. TNF receptor mediated Assembly of DD and FADD
2. autocleavage of procapse 8
3. CASP8 cleavage of procapse 3
4. CASP3 cleavage of cellular proteins

Question 14

Cell survival pathway

Answer 14

-TRAF2
active p50/p65 heterodimeric NFkB translocated to the nucleus

Question 15

Lipids and Fatty acids Melting point

Answer 15

-the more carbons that you add, the higher the MP
-The more cis bonds that you add, the lower the MP

Triacyglyerols- TAGs, used for energy storage, has 3 fatty acids and a glyererol.

Question 16

Triacyglycerols are energy storage lipids

Answer 16

Come from
1. diet-carried in chylomicrons
2. liver synthesis-carried in VLDL
3. adipocytes- with albumin

Question 17

TAGS synthesized in the liver are packages in VLDL particles, how does this work?

Answer 17

triacyl biosynthesis uses acetyl-coa and proteins to generate palmitic acid in cytosol. this gets converted to TAG

1. Liver VLDL particles are assembled in the endomembrane and then pacakged into secretory vesicles and exported to the circulatory system.
2. liver cells synthesize cholesterol from acetyl-coa, which is also packaged into VLDL as cholesterol esters
3. VLDL particles deliver the TAGs to tissue through the body

Question 18

TAGS through diet

Answer 18

start in the intestine

1. dietary emulsification of TAG by bile acids.
2. hydrolysis of Tag by intestinal lipases to generate free fatty acids.
3. resynthesis when inside intestinal
4. gets packaged into chylomicron and goes to lymphatic system
5. entry of chylomicron into the circulatory system though subclavian vein.

Question 19

Release of Fatty Acids

Answer 19

ApoC-II on the surface of chylomircon binds and activates lipoprotein lipase

causes endothelial cell to release glycerol and fatty acids

fatty acids diffuse into endothelial cells and go to nearby adipose and muscle cells

leads to formation of albumin-fatty acids complex

Question 20

Glucagon signaling stimulates fatty acids release

Answer 20

Glucagon signaling in adipocytes stimulates release of FFA from TAGs stored in lipid droplets.

PKA phosphorylates perilipin, which promotes binding of G58 to adipose triglyceride lipase.

FFAs released by lipase cleavage are sequestered by human adipocyte fatty acid binding protein 4 and then exported to the circulatory system, where they are transported to peripheral tissues by albumin.

Question 21

Lipids function in cell signaling

Answer 21

-steroids and Eicosanoids

hydrophobic property of lipids contributes to their function as higher affinity sterospecific ligands

Question 22

Steroid hormones

Answer 22

Mediate hormone signals by altering the expression for specific genes

-glucosteroids, minerialsteroids, estrogens, androgens

cortisol: adrenal cortex, functions with liver metabolism, immune function, and adaption of stress.

Aldosterone: Adrenal cortex, Ion transport in the kidneys, BP regulation.

Question 23

Eicosaonoids

Answer 23

Group of signaling molecules derived from C20 polyunsaturated FA

-modified by mitochondrial enzymes

prostaglandins, prostacyclins, thromboxane and leukotrines

Question 24

NSAIDS and Eicosanoids

Answer 24

Derived from arachidonate

activation of GPCR leads to stimulation of PLA activity, this releases arachidonate

Cox-1 and cox-2 are inhibited by anti-inflammatory drugs like NSAIDS.

*uses Lipoxygenase to convert to eicosanoids

Question 25

Key enzymes involved in Fatty Acid metabolism

Answer 25

FA metabolism:
-fatty acid acyl- coa synthetase; catalysis “priming” reaction in fatty acids metabolism; converts FFA in the cytosol into fatty acyl-coa

FA Oxidation:
-carnitine acyltransferase I
catalyzes the rate-limiting step in fatty acid oxudation.

FA synthesis:
-Acetyl-CoA carbosylase
catalyzes rate-limiting step in fatty acid synthesis.

Fatty acid synthase
catalyzes series of reactions that add C2 units to a growing fatty acid chain

Question 26

Carnitine Transport Cycle

Answer 26

• 3-step process that translocates fatty acids across the inner mitochondrial membrane

1. Carnitine acyltransferase I limks carnitine to palmitoyl-coA and releases CoA
2. The carnitine- acylcarnitine translocase protein in the inner mitochondrial membrane exchanges palmitoylcarnitine for carnitine
3. carnitine acyltransferase II replaces carnitine with CoA

Question 27

Ketogenesis: a salvage pathway for acetyl-coA

Answer 27

Salvages acetyl-coA from liver mitochondria and converts it to acetoacetate and D-B-hydroxybutane, which are exported to skeletal and cardiac muscle where they are used for energy conversion.

*occurs during starvation while carbohydrate sources are limited or when glucose homeostasis is defective in the case of diabetes.

1. Oxaloacetate diverted to make glucose through pyruvate and goes to brain
2. Buildup of acetyl-coA
3. Using ketogenesis the excess acetyl-coA is converted to ketone bodies, like the acetoactate and hydroxybutane.

Question 28

Synthesis of Fatty acids and TAGs

Answer 28

3 steps: glycolysis, citrate shuffle and fatty acid synthesis

Excess glucose from eating too many nonfat high carb foods is converted to triacyglyerol in hepatocytes and exported to adipose tissue in VLDL

under conditions of excess carbs. in the liver, flux through citrate cycle is inhibited by high energy charge in the cell, thereby stimulating citrate export from the mitochondrial matrix.

Question 29

Differences b/w fatty acid degradation and synthesis

Answer 29

Commons:
-4 step reaction cycle
-Each step involves removal or addition of C2 units

Differences
-place of synthesis
-number of enzymes
-rate-limiting step

degradation
*oxidation, hydrolysis, oxidation, cleavage
*occurs in mitochondrial matrix
*Multiple enzymes
*Carnitine is rate limiting

Synthesis
*condensation, reduction, dehydration, reduction
*in cytsol
* 2 enzymes
* Malonyl-CoA is rate limiting

Question 30

Acetyl-CoA carboxylase activity is stimulated by protein polymerization

Answer 30

1. metabolic regualtion, od acetyl-coA is mediated by citrate and palmitoyl-CoA, which are allosteric regulators that bind to the enzyme and alter the equilibrium between active and inactive
2. Hormonal regulation, by insulin which causes dephosporylation and polymerization of acetyl-CoA carboxylase through activation of protein phosphatase
   Glucagon stimulates phosphorylation of

Question 31

lipoprotein transport

Answer 31

transport throughout the entire body and function to control cholesterol hemostasis by regulating, recycling and output of cholesterol on a daily basis.

*3 sources of cholesterol are dietary, biosynthesized in liver, and stored in peripheral tissues.

Question 32

Watson-crick base parings in DNA

Answer 32

C&G- keto vs. enol

A&T- amino vs. imino

A and C have PkA around 4
G and T have PKA around 10