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5100 Foundations > Week 1 Biochem > Flashcards

Week 1 Biochem Flashcards

1
Q

types of DNA error/mismatch repair

1.

2.

A
  1. DNA Pol II proofreading and exonuclease activity during replication
  2. relies on MSH proteins sfter replication - recruits endonuclease and exonuclease - removese a segment of one strand
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2
Q

Types of damage repair (not error repair)

1.

A
  1. Base excision repair (BES) - used to fix damage from harmful chemicals (commonly, deamination)
  2. Nucleotide Excision repar (NER) - used when there is damage from physical agents (causing pyrimidine dimers)

*deamination = removal of amino group from nitrogenous base which converts the base into a different molecule.

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3
Q

which base most commonly undergoes spontaneous deamination?

A

cytosine

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4
Q

Ionizing radiation causes what kind of damage

A

double stranded breaks.

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5
Q

How do you repair the damage caused by ionizing radiation that left a jagged double stranded break

1.

2.

A
  1. Non-homologous end joining - uses protein “artemis” to cut off the overhanging ends of damaged DNA then the two ends are ligated together– error prone repar mechanism since you are getting rid of genetic material
  2. homolous recomindation - uses the sequence of a sister chromatid as a template for - more reliable repair mechanism - no loss of nucleotides
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6
Q

H&E staining refers to ?

what gets stained what color and why?

A

Haemotoxylin & eosin

H is basic and dies the nucleic acids because they are acidic

E is acidic and dies basic structures along the gradient of red to pink

mnemonic:

H/B are consonants. E/A are vowels

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7
Q

what is the nucleolus

a _____________ compartment in the nucleus that is the site of ___________

A

a non-membrane bound compartment

site of ribosomal RNA synthesis (in their immature forms)

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8
Q

y or n - can you see the cell membrane with light microscopy

A

no

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9
Q

what are the types of microscopy used in viewing cells

1.

2.

A
  1. staining + light microscopy - colored - based on acid base chemistry
  2. electron microscopy -black and white -based on whether a structure is dense enough to block electrons (nucleus and nucleolous are black bc they are so dense. You CAN see organelles and cell membrane
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10
Q

T or F: There is no relation between the amount of cholesterol in the cell and cholesterol that builds up on vessels in atherosclerosis

A

T

Even if you have too much cholesterol in your blood, you still have the right amount of cholesterol in the cell membrane

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11
Q

where in the cell are alcohol dehydrogenases (ADH) located?

A

cytosol

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12
Q

what is the disulfiram-alcohol reaction?

A

alcohol is broken down into acetaldehyde. disulfiram (Antabuse) blocks the normal conversion of acetaldehyde into H+ and acetyl radical, causing a massive increase in accumulation of acetaldehyde.

Clinical: DON’T administer antabuse to a patient who has alcohol intoxication. they need to wait till the alcohol in their sytem is metabolized

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13
Q

what are the 3 enzymes in the cell that convert alcohol to acetaldehyde?

A
  1. ADH (alcohol dehydrogenase)
  2. Cytochrome p450 - located in smooth ER
  3. catalase - located in peroxisomes
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14
Q

what is the difference between a peroxisome and lysosome?

A

They differ from lysosomes in the type of enzyme they hold. Peroxisomes hold on to enzymes that require oxygen (oxidative enzymes). Lysosomes have enzymes that work in oxygen-poor areas and lower pH. Peroxisomes absorb nutrients that the cell has acquired.

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15
Q

what are the types of repair mechanisms for errors or damage to DNA?

A
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16
Q

The hormones utilizing the cAMP mechanism can be remembered with the mnemonic

FLAT CHAMP uses CHEGG

A

FSH

LH

ACTH

TSH

CRH

hCG

ADH (V2 receptor)

MSH

PTH

Calcitonin

Histamine (H2)

Epinephrine

GHRH

Glucagon

Norepinephrine

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17
Q

Spindle poisons include:

1.

2.

3.

A
  1. Colchicine, which inhibits microtubule polymerization,
  2. vinca alkaloids
  3. taxanes

^used for gout and cancer treatments and arrest mitotic division

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18
Q

what is significant about low substrate concentrations (before saturation) in enzyme kinetics?

A

Initially, at low substrate concentrations, the rate of the reaction (V) increases as the substrate concentration increases. As the substrate concentration continues to increase, the enzyme will eventually become saturated and the rate of the reaction will plateau at Vmax, the maximum rate at which the reaction can occur.

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19
Q

The Golgi apparatus function

A

The Golgi apparatus is an organelle consisting of flattened membrane disks that functions to:

process newly synthesized proteins. Folded proteins contained in vesicles travel along microtubules and are brought to the Golgi apparatus for glycosylation or modification.

From the Golgi apparatus, modified proteins are once again transported via microtubules enclosed within vesicles.

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20
Q

Cardiac glycosides (aka digitalis) inhibit ____________

A

Na+/K+-ATPase

e.g. Digoxin (plant-based medication), Ouabain (poison)

functions by inhibiting the Na/K-ATPase, so intracellular sodium levels ↑ and intracellular potassium ↓. Because calcium export depends on a Na+/Ca2+ exchanger, intracellular calcium also ↑. The overflow calcium goes to the sarcoplasmic reticulum, improving cardiac contractility. (also decreases AV conduction and heart rate)

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21
Q

Hemachromatosis –> possible iron accumulation in joint space –> triggers deposition of _____________ in the joints.

Potential treatment:

A

calcium pyrophosphate dihydrate crystals (CPP).

Patients with HH demonstrate the full spectrum of CPP deposition, including chondrocalcinosis, chronic degenerative arthritis, and acute arthritis (pseudogout).

Oral medications include nonsteroidal antiinflammatory drugs, such as indomethacin, colchicine, and in some cases corticosteroids.

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22
Q

Colchicine is a drug that treats pseudogout. How does it work?

A

the drug accumulates in neutrophils, binds to tubulin and interferes with microtubule polymerization. This prevents migration of neutrophils into the joint space and decreases inflammation.

Other microtubule inhibitors (vincristine, vinblastine) also block polymerization of microtubules in mitotic spindle formation and function as powerful chemotherapeutics.

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23
Q

Gout vs pseudogout

A

While gout is caused by uric acid crystals; pseudogout is caused by calcium pyrophosphate dehydrate crystals (CPPD). And though the two have similar symptoms, treatment is somewhat different. Pseudogout causes sudden attacks of joint pain, swelling, and warmth. The attacks can last for days to weeks.

medication that prevents reabsorption of uric acid in urine (uricosurics) can be indicated for chronic management of gout but has no role in the management of pseudogout.

Colchicine, NSAIDs, and corticosteroids are the medications of choice for acute pseudogout and gout attacks.

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24
Q

The NF-kB pathway has been found to be physiologically important in _____________

A

immune modulation, acute phase inflammatory response, cell adhesion, differentiation, and apoptosis. NF-kB inhibitors, such as sulfasalazine, include a growing class of anti-inflammatory medications and are indicated for control of autoimmune diseases, such as Crohn’s disease. NF-kB inhibition is not the mechanism of action of colchicine.

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25
von Hippel Lindau (VHL) syndrome is a ____________ \_\_\_\_\_\_\_\_\_\_\_\_ disease and is the result of deletion of the VHL gene on chromosome 3.
autosomal dominant VHL syndrome is characterized by excessive angiogenesis manifesting as 1. cavernous hemangiomas in the skin (the patient’s non-blanching, spongy skin lesion) and 2. hemangioblastomas in the central nervous system, commonly in the cerebellum (causing ataxia), retina (causing vision problems), brainstem, and spine.
26
T/F: Loss of adhesion to the basement membrane is a key step in the formation of a carcinoma becoming metastatic. In order for neoplastic cells to enter the bloodstream or lymphatic channels, cells must first break away from anchorage on the basement membrane.
TRUE
27
between trans and cis unsaturated fatty acids, which promote greater membrane fluidity
In terms of fatty acid structure, fatty acids in the cis formation exaggerate the kink produced by double bonds when compared to the trans formation, making the cis formation more fluid than the trans isomer.
28
Proper functioning of the mitotic spindle is a prerequisite for chromosome transportation. Inhibition with spindle poison leads to arrest of mitosis and cessation of cell division. Spindle poisons include \_\_\_\_\_\_\_\_\_, \_\_\_\_\_\_\_\_\_, and \_\_\_\_\_\_\_\_\_\_\_
colchicine, which inhibits microtubule polymerization, as well as vinca alkaloids and taxanes.
29
Role of p53 protein
tumor suppressor: prevents cells with genetic errors from entering the S phase of the cell cycle by activating p21 or p27 (more commonly p21) p21 is a phosphoprotein that inhibits Cdks → Cdk-mediated phosphorylation of pRb is decreased → pRb becomes active and binds transcription factor E2F → entry into the S phase cannot occur
30
G1 Cell cycle checkpoint is regulated by:
Regulated by the **[p53](https://www.amboss.com/us/knowledge/The_cell_cycle#xid=Mo0McS&anker=Z78f5b8ce73420dd5301a753625b67c7c)** protein and the **[cyclin D/Cdk4 complex](https://www.amboss.com/us/knowledge/The_cell_cycle#xid=Mo0McS&anker=Zb7852fd328b06c8ef18617b4fd03b8ca)**, which both affect the activity of the **[retinoblastoma protein](https://www.amboss.com/us/knowledge/General_oncology#xid=WM0Png&anker=Z0ead16e0f60341282ccee14cec91c6da)** ([pRb](https://www.amboss.com/us/knowledge/General_oncology#xid=WM0Png&anker=Z0ead16e0f60341282ccee14cec91c6da)).
31
nucleotide excision repair occurs in the \_\_\_\_\_\_\_\_\_\_phase and is absent in people with \_\_\_\_\_\_\_
G1 phase Xeroderma pigmentosum
32
The progress of a cell through the cell cycle is largely regulated by two key classes of molecules:
Cyclins bind to CDKs and activate them, which in turn phosphorylate target proteins. Phosphorylation can either activate or inactivate target proteins to coordinate progress through the cell cycle. CDKs are always expressed within the cell, waiting for cyclins to be synthesized in response to various molecular signals.
33
In addition to regulating progression of the cell cycle at the G1/S checkpoint, p53 regulates the cell cycle by:
initiating repair of damaged DNA, inducing apoptosis
34
Rb is a tumor suppressor protein that prevents cell cycle progression at the G1/S checkpoint in its active state (dephosphorylated). Its activity is largely regulated by cyclin ______ (with CDKs).
Cyclin D Cyclin D complexed withe CDKs, phosphorylate Rb to pRb, leading to the inactivation of Rb. This process allows cells to enter into the cell cycle state. When Rb becomes phosphorylated, the cell can enter S phase. Rb does not influence p21 levels.
35
Rb protein is a key regulator of the G1/S cell cycle checkpoint. It is a tumor suppressor that halts cell cycle progression by _activating/inactivating_ E2F
inactivating E2F are transcription factors that (when active) induce the expression of S phase genes. The Rb protein itself is inhibited by cyclin-CDK complexes; as such, these cyclin-CDK complexes are pro-progression.
36
At which location does the axillary artery continue as the brachial artery?
inferior border of the teres major
37
Cdk-mediated phosphorylation of Rb activates or inactivates Rb?
inactivates --\>releases previously bound transcription factor E2F → initiates the transcription of numerous genes that are required for DNA replication
38
anaphase vs telophase
In anaphase, sister chromatids (now called chromosomes) are pulled toward opposite poles. In telophase, chromosomes arrive at opposite poles, and nuclear envelope material surrounds each set of chromosomes. Finally, in cytokenesis, the two daughter cells are separated.
39
40
What molecule is synthesized in the rate-limiting step of cholesterol de novo synthesis?
mevalonate
41
cholesterol is used for what purposes
1. component of bile salts 2. used to synthesize vitamin D 3. synthesis of steroid hormones NOT involved in fatty acid synthesis
42
what is the key carbon in cholesterol (the one that gets esterified)
Carbon 3 (esterification = fatty acid addition)
43
What lipoprotein does not contribute to total plasma fasting cholesterol?
chylomycron because they are only present after a meal
44
where is cholesterol synthesized
in the cytosol and ER of all nucleated cells
45
what is the mechanism of action of statins?
competitively inhibits HMG CoA Reductase with is the first step (committed step) in the conversion of acetyl Co-A to downstream intermediates (notably farnesyl and melavonate) and ultimately cholesterol.Doing so upregulates the synthesis of LDL receptors, increasing uptake by cells
46
potential side effects of statins
farnesyl is an intermediate in the cholesterol synthesis pathway that is a precursor for: coenzyme Q Protein farnesylation Dolichol Heme-a (complex IV) therefore statin side effects can include reductiiion of all of the above
47
insulin __________ activity of HMG Co-A Reductase whereas glucagon _______ its activity (up or down regulation)
insulin increases activity of HMG Co-A Reductase whereas glucagon decrease its activity because insulin indicates an excess of glucose/acetyl CoA
48
HMG CoA is the product of
2 molecules of Acetyl CoA
49
LCAT vs ACAT
LCAT esterifies cholesterol in the plasma ACAT esterifies cholesterol in liver cells
50
what are thee 4 regulatory mechanisms controls HMG-CoA reductase activity
reg controls indicated by red numbers
51
what are SREBPs
they are sterol regulatory element binding proteins they are a familiy of tx factors that control expression of several enzymes that regulate synthesis of all of FAs, triacylglycerol, phospholipids, notably **HMG CoA Reductase**
52
In addition to cholesterol, chilomicrons also carry
Vitamins, ADEK and Triglycerides
53
what are the different proteins involved in each type of cell to cell adhesion complex: 1. zona occludens 2. zona adherena 3. desmosomes 4. gap junctions 5. hemidesmosomes
notice that hemidesmosomes and desmosomes don't use the same protein
54
what changes characterize IRREVERSIBLE cell injury
55
COP I vs COP II
56
In a patient taking prescription medication for a chronic disorder, a histological section of a liver sample from the patient is labeled for reactivity to cytochrome p450. Under an electron microscope, in what organelle would you expect the label to be seen?
Mnemonic: Smoothness --\> lipid (which is smooth) metabolism and "Smooth" starts with same sound as "Cytochrome p450"
57
What is spectrin
Spectrin is an intracellular cytoskeletal protein that lines erythrocyteplasma membrane of red blood cells, and helps to maintain cell membrane integrity i.e. biconcave shape of red blood cell. Spectrin deficiency affects membranen integrity and leads to red blood cells that are rounded in appearance (spherocytosis)
58
nuclear lamina is formed from
nuclear lamin protein - a subunit protein of intermediate filaments
59
how does pyruvate get into the mitochondria
transported by: Mitochondrial Pyruvate/H+ Carrier (MPC) sends Pyruvate to the matrix
60
net products of TCA
61
Exposure to Arsenate (Arsenic acid, H3AsO4), an environmental toxin, inhibits \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_.
GAPDH in glycolysis
62
Luebering-Rapapport Shunt
In biochemistry, the Luebering–Rapoport pathway (also called the Luebering–Rapoport shunt) is a metabolic pathway in mature erythrocytes involving the formation of 2,3-bisphosphoglycerate (2,3-BPG), which regulates oxygen release from hemoglobin and delivery to tissues. this has nothing to do with regulation of glycolysis it has to do with homeostasis in low oxygen environments
63
what are all the effects on the immune system that antibodies can have?
64
how does each TYPE of inflammation determine the differentiation of Th cells
65
how to calculate BMI
66
what are some organisms that the spleen is responsible for phagocytosing?
2 categories: 1. encapsulated bacteria 2. parasites that are blood-borne
67
what is digeorge syndrome
Thymic epithelium fails to develop; T cells do not mature – Mutation in Tbx1 gene – Absence of thymus (No T cells) therefore they have a lot of infections also have cardiac abnormalities
68
encapsulated bacteria can evade all parts of the immune system. True or false
FALSE: Capsules made of polysaccharides permit bacteria to evade phagocytosis by **macrophages alone.** The clearance of capsulated bacteria is greatly facilitated by complement and IgG opsonization
69
what are the CDK/Cyclin complexes and at what stage of replication do they operate
70
granuloma question
Granuloma is a pathological appearance of a certain type of inflammation that is chronic. it occcurs when macrophages attempt to sequester a pathogen that they cannot phagocytose
71
role of interferon gamma in granuloma formation
72
what is biofilm growth

5100 Foundations (12 decks)

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