Biochem Flashcards by Brett Niles

Describe long range, hormone signaling via the blood

Endocrine signaling, it is long lasting (on the minutes scale)

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Describe paracrine signaling

The signals are called paracrine factors
They diffuse to neighboring cell of a different cell type
They are short lived
Important in neurotransmission

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Describe autocrine signaling

Common in growth factors for cancer

Cells self stimulate

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Describe direct or juxtacrine signaling

Signal binds to cell that is is in contact with

Immune cells use this

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Lipohillic signals are ______ lived and they have what 2 receptors

Long, cytoplasmic and nuclear

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What are some common lipophilic and hydrophilic medications

Lipo-contraceptives

Hydro-epinephrine

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Graves’ disease causes ____________ and presents with decreased _____ and increased _______

Hyperthyroidism, TSH, T3 and T4

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What are the symptoms of Graves? Who does it affect? What are some treatments?

Weight loss, tachycardia, insomnia, thyroid goiter, “buggy eyes”
Women, presents by 40
Resection of the thyroid, radioactive iodine, and pharmacological intervention

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The TMD of G-protein-coupled receptors have 7 _______ that are arranged in a _________ pattern. The ECD relies on _________ bonds

Alpha helices, circular, disulfide

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________ activate G proteins while ___________ inactivate them

GEF, GAP

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______________ proteins produce secondary messengers

Effector

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Gs, Gi, Gt, and Gq are activated by or activate what?

Activates AC->cAMP activates PKA
Inhibits AC
Activated by light; activates cGMP PDE (cGMP->GMP)
Activates PLC; IP3 opens Ca channel on SR or ER

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Caffeine affects what?

Inhibits cAMP PDE -> increased cAMP since breakdown is slowed

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Albuterol is a ____________ which activates ________________ receptors. What is one side effect of its use for asthma?

Beta agonist, beta-adrenergic, increased HR

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What is the MoA of cholera toxin?

Decreased GTPase activity
Gsa remains active and therefore AC keeps producing cAMP, this keeps intestinal Cl- channels open, Cl- leaves and water follows

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What is the MoA of pertussis?

Gia prevents dissociation of alpha subunit from G protein complex -> less inhibition of AC ->too much cAMP->lots of fluid and excess mucous in airways

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How are GLUT4 and G proteins similar?

They can both be sequestered in vesicles when not needed. GPCR can even be degraded

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What is another mechanism to control GPCR response without sequestering them?

Phosphorylation of GPCR which causes arrestin to bind

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Phopshotyrosine is recognized and bound by the adapter and docking protein _______________.

SH2 domain of Grb2

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Binding of substrate to RTK causes a conformational change followed by ________________

Autophosphorylation

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There are RAS dependent and RAS independent pathways associated with RTK. What do they do?

RAS dependent cause changes in gene transcription

RAS independent cause changes in protein and enzyme activity

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JAK STAT receptors offer a more __________ route to altering __________

Direct, transcription

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STAT goes to the _____________ after activated

Nucleus

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What kind of molecules bind to JAK STAT receptors?

Cytokines

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RAS mutations are linked to ___________

Cancer

_________ blotting uses DNA probes and targets DNA

Southern

_____________ blotting involves a ssDNA probe and targets mRNA

Northern

Western blotting is used for early detection of _____

HIV

Western blotting targets ____________

Protein

What is the target of Eastern blotting?

Post-translational modifications of proteins (lipids, carbs, phos., etc.)

One of the main purposes of PCR is early detection of micro organisms responsible for what diseases

HIV, bacterial and fungal infections that cause Lyme disease

What does PCR allow us to do? What are the three main steps?

Amplify isolated DNA 1. Heat 2. anneal 3. extend

VNTR are used to detect what 3 diseases?

Huntington disease, Fragile X, Frederick Ataxia

ELISA should be used to confirm HIV in what time period? What can be used to confirm? Why is confirmation needed?

4-6 weeks Western blotting ELISA can give both false-positives and false-negatives

What does VNTR do in layman's terms?

Shows how many copies of a repeated section are present

What are the two types of ELISA and what are they used for?

Indirect - measures amount of Ab in a sample Sandwich - measures the amount of antigen in sample

ELSA can be used to detect ________________ commonly found post MI

Troponin

What are the 3 general stages of the cell cycle? And what do they do?

Mitosis - nuclear division at beginning and cytokinesis at the end Interphase - G1 -RNA and protein synthesis needed for DNA replication S - DNA synthesis G2 - DNA stability is checked G0 - poor nutrient/environmental conditions (brain, cardiac muscle, RBC)

What happens during G1 phase?

RNA and protein synthesis | Cell growth

What happens during S phase?

DNA replication Histone synthesis Centrosome formed Chromosomes duplicate

What happens during G2 phase?

preparation for mitosis

What happens during M phase?

Mitosis (PMAT) and cytokinesis

Where is the restriction point? What is it dependent on?

Before G1 checkpoint towards the end of G1 | Growth factors

What is the checkpoint at the end of G1?

DNA damage check

What is checked at the end of G2?

Verify complete genomic duplication

What happens during the metaphase checkpoint?

Checks to make sure chromosomes are attached to the mitotic spindle

What activates cyclin-CDK?

CAK phosphorylates the cave site | CDC25 phosphatase removes an inhibitory phosphate from the roof site

What inhibits cyclin-CDK complex?

P27 binds to it | WEE1 kinase adds an inhibitory phosphate to the roof site

What is the function of the T-loop?

It serves as a regulation mechanism and only moves out of the active site after cyclin binds This site is then phosphorylated by CAK (the cave site)

What cyclins are linked to what stage?

G1 - D G1/S - E S - A M - A/B

Besides levels of phosphate, how else can you inhibit cyclin-CDK?

binding of P27

What is one way the M cyclins are regulated?

Ubiquitinylation --> degradation by proteosomes

How does P53 protect the cell? What is it normally inhibited by?

It leads to increased transcription of p21 which then binds to CDK-complexes and causes cell cycle arrest P53 is normally inhibited by MDM2 which is a ubiquitin ligase

P53 activity can lead to what two outcomes

1. Reparable damage leads to cell cycle arrest and DNA repair 2. Irreparable damage leads to apoptosis pathway

What are the general apoptosis pathways? What causes them?

1. Extrinsic binding (TNFalpha and Fas) | 2. Intrinsic (leakage of Cyt C from mito)

What caspase does the extrinsic pathway activate?

Caspase 8 (it starts in the pro-caspase form)

What are the two major classes of caspases? What caspases are involved?

Initiatiors (caspase-8 and caspase-9) | Executioners (caspase-3)

Is BAX pro or anti-apoptotic? How does it work?

Pro-apoptosis | Active BAX proteins aggregate in the mito membrane and form a pore for proteins to be released through into the cytosol

What activates Apaf1?

The binding of mitochondrial Cyt C | It then forms an apoptosome which activates Caspase-9

What is the difference between a proto-oncogene and an oncogene?

Proto-oncogenes have the potential to cause cancer if they undergo gain of function mutations These genes are generally responsible for normal cell growth and division

What mutation in HER2 causes cancer? What cancer does it cause?

Change in TMD from a Val to Gln, this causes dimerization and ultimately RTK activity Breast

Heterozygosity for the RB protein causes what?

Cells to be predisposed to cancer (requires another hit)

What are some cancer associated viruses?

Epstein Barr, HepB, HPV, Kaposi Sarcoma

What anticancer inhibits BCR-ABL fusion protein?

Gleevec

What is the MoA of herceptin?

Ab (the drug) binds to disallow dimerization, assists immune cells in recognizing cancer cells, and can lead to endocytosis and degradation

What is the MoA of gleevec?

It doesn't allow ATP to bind to BCR-ABL fusion protein

Lipophilic signals are carried in the blood by ____________________

Carrier proteins