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Biochemistry FA > Molecular + cellular > Flashcards

Molecular + cellular Flashcards

0
Q

Checkpoints control transition between phase of cell cycle. Is regulated by:

A

Cyclins
Cycle - dependent kinases (CDK)
Tumor suppressor

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1
Q
  1. Which is the shortest phase of cell cycle?.

2. which phases are variable?

A
  1. Mitosis

2. G1 and G0

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2
Q

What is G and what is S in cll cycle

A

Gap

Synthesis

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3
Q

M phase includes

A
  1. mitosis (Prophase, Metaphase, Anaphase, Telophase)

2. cytokinesis (cytoplasm splits in 2)

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4
Q

Which cell cycle regulator is CONSTITUTIVE AND INACTIVE

A

Cyclin dependent kinases (cdk)

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5
Q

Which cell cycle regulators are phase specific?

Role?

A

Cyclins….activate cyclin dependent kinases (CDKs)

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6
Q

Phases of cell cycle:

What is interphase?

A
  1. G1 (and G0)
  2. S phase
  3. G2
  4. M phases

Interphase: G1-S-G2

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7
Q
  1. Tumor suppressors in cell cycle regulation (mechanism)

2. If mutated:

A
  1. P53 induce p21 which HYPOphosphorylates Rb –> binds to and inactivate E2F –> Inhibit G1 to S progression
  2. Unrestrained cell cycle division (eg Li-fraumeni)
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8
Q

Which cell type is affected by chemotherapy

A

Labile

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9
Q

Cell types according their proliferative ability: (and definition)

A
  1. Permanent - remain in G0, regenerate from stem cells
  2. Stable (quiescent) - enter G1 from G0 when stimulated
  3. Labile: never go to G0, divide rapidly with shirt G1. Most affected by chemotherapy
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10
Q

Cell type that is also called QUIESCENT

A

Stable

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11
Q

Permanent cell examples

A

Neurons, skeletal and cardiac muscle, red blood cells

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12
Q

Stable (quiescent) cells examples

A

Hepatocytes, lymphocytes

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13
Q

Labile cells examples

A

Bone marrow, gut epithelium, skin, hair follicles, germ cells

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14
Q

Smooth vs rough

Endoplasmic reticulum according their structure:

A

Smooth endoplasmic reticulum LACKS SURFACE RIBOSOMES

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15
Q

Cell type with short G1

A

Labile

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16
Q

Smooth endoplasmic reticulum role:

A
  1. Steroids synthesis

2. Detoxification of drugs and poisons

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17
Q

Cells rich in smooth endoplasmic reticulum:

A
  1. Liver hepatocytes
  2. Steroid hormones-producing cells of the adrenal cortex
  3. Steroid hormones-producing cells of the gonads
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18
Q

Cells rich in rough endoplasmic reticulum

A
  1. Mucus-secreting goblet cells of the small intestine

2. Antibody-secreting plasma cells

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19
Q

Rough endoplasmic reticulum role:

A
  1. Synthesis of secretory (exporter) proteins

2. N-linked oligosaccharides addition to many proteins

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20
Q

What are Nissl bodies and what is their function

A

Nissl bodies are rough endoplasmic reticulum in neurons

Synthesize peptide neurotransmitters for secretion

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21
Q

Free ribosomes (structure and function):

A

Unattached to any membrane

Site of synthesis of cytosolic and organelle proteins

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22
Q

Proteasome stracture and function

A

Barrel-shaped protein complex that degrades damaged or UBIQUITIN-tagged proteins

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23
Q

Ubiquitin - Proteasome system defects:

A

It have been implicated in some cases of PARKINSON disease + Alzheimer
Genes (parkinin, PINK1, DJ-2)

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24
Q

Peroxisome structure

A

Membrane enclosed organelle

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25
Q

What is Golgi apparatus?

A

Is the distribution center for proteins and lipids from the endoplasmic reticulum to the vesicles and plasma membrane

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26
Q

Peroxisome function:

A

Catolism of:

  1. Very-long-chain fatty acids
  2. Branched chain fatty acids
  3. Amino acids
  4. ethanol
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27
Q

Golgi apparatus function:

A
  1. Modifies N-oligosaccharides on ASPARAGINE
  2. Adds O-oligosaccharides on SERINE and THREONINE
  3. Adds MANNOSE-6-PHOSPHATE to proteins from trafficking to lysosomes
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28
Q

Endosomes?

A

Sorting centers for materials from OUTSIDE the cell or from the GOLGI sending it to lysosomes for destruction or back to membrane/Golgi for further use

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29
Q

I-cell disease (inclusion cell disease also referred to as:

A

Mucolipidosis II

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30
Q

which enzyme is defective in inclusion cell disease and and what is the problem? What is low?

A

Phosphotransferase
Failure of Golgi to phosphorylate mannose residues
LOW LEVELS OF MANNOSE RESIDUES

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31
Q

I cell disease (inclusion cell disease) pathophysiology:

A

Inherited lysosomal storage disorder- defect in N-acetylglucosamil-1-phosphotranferase - failure of the Golgi to phosphorylate mannose residues (LOW MANNOSE-6-PHOSPHATE) on glycoproteins - proteins are secreted extracellularly rather than delivered to lysosomes

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32
Q

I cell disease (inclusion disease) results

A
  1. Coarse facial features
  2. Clouded corneas
  3. Restricted joint movements
  4. High levels of lysosomal enzymes
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33
Q

Is i-cell disease - course

A

I - cell disease is OFTE FATAL IN CHILDHOOD

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34
Q

Signal recognition particles (SRP):

A

SRP are abundant, cytosolic ribonucleoproteins that traffic proteins FROM THE RIBOSOME TO THE ROUGH ENDOPLASMIC RETICULUM

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35
Q

Absent or dysfunctional Signal recognition particles (SRPs)

A

Proteins accumulate in the cytosol

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36
Q

Golgi phases:

A
  1. Endoplasmic reticulum phase - cis phase

2. Plasma membrane phase - trans phase

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37
Q

Vesicular trafficking proteins:

A
  1. COPI
  2. COPII
  3. Clathrin
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39
Q

COPI function:

A

Vasicular trafficking protein:

  1. Golgi to cis Golgi (retrograde)
  2. cis Golgi to Endoplasmic reticulum
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40
Q

COPII function:

A

Vasicular trafficking protein:

Endoplasmic reticulum to cis Golgi (anterograde)

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40
Q

Clathrin associated plasma membrane to endosomes:

Example:

A

Receptor mediated endocytosis

Example: LDL receptor activity

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41
Q

Clathrin function:

A

Vasicular trafficking protein:

  1. Trans-Golgi to lysosomes
  2. Plasma membrane to endosomes (receptor mediated endocytosis)
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42
Q

what is the proportion for each ATP molecule:

A

For each ATP, 3 Na go out and 2 K come in

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43
Q

Where is sodium potasium pump located and where is its ATP site?

A

Sodium - Potasium pump is located in the plasma membrane with ATP site on cytosolic side

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44
Q

Sodium potassium pump function:

A
  1. 3 Na bind on the cytosolic side
  2. 3 Na are released on the extracellular side and the cytosolic site hydrolyzes ATP to ADP ( Pi is linked to the pump)
  3. 2 K bind on the extracellular site of the pump and Pi is released from the pump
  4. 2 K are released in the cell
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45
Q

3 Drugs that inhibit sodium-potassium pump:

A
  1. Quabain
  2. Digoxin
  3. Digitoxin
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46
Q

Quabain mechanism

A

Quabain inhibits sodium potasium pump by binding to K site

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47
Q

Digoxin and Digitoxin mechanism of action:

Which is their indirect effect?

A

Digoxin and digitoxin directly inhibit sodium-potassium pump. That leads to indirect inhibition of the sodium calcium exchanger- high intracellular calcium concentration- cardiac contractility

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48
Q

Most abundant protein in human body and its general function

A

Collagen - organizes and strengthens extracellular matrix

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49
Q

Which protein is responsible to organizes and strengthens extracellular matrix?

A

Collagen

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50
Q

How does collagen take its final conformation?

A

Extensively modification by post-translational modification

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51
Q

Most common type of collagen

A

Type 1. (90%)

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52
Q

Which cells product collagepn type 1 in bones?

A

Osteoblasts

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53
Q

Collagen type 1 is founded to:

A
  1. Bone
  2. Skin
  3. Tendon
  4. Dentin
  5. Fascia
  6. Cornea
  7. Late wound repair
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54
Q

Disease of low production of collagen type 1

A

Ostogenesis imperfecta type 1

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55
Q

What is reticulin

A

Is a type of fiber in connective tissue composed of type III collagen secreted by reticular cells. Reticular fibers crosslink to form a fine meshwork (reticulin). This network acts as a supporting mesh in soft tissues such as liver, bone marrow, and the tissues and organs of the lymphatic system

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56
Q

Collagen type 2 is founded to:

A
  1. Cartilage (including hyaline)
  2. Vitreous body
  3. Nucleus pulposus of intevertebrate discs
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57
Q

Where is type 3 collagen founded?

A
  1. Skin
  2. Blood vessels
  3. Uterus
  4. Fetal tissue
  5. Granulation tissue
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58
Q

Type 3 collagen deficiency:

A

Vascular type of Ehlers - Danlos syndrome (uncommon)

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59
Q

2 disease associated with collagen type 4

A
  1. Alport syndrome

2. Goodpasture syndrome

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60
Q

Defective of collagen type 4

Clinical symptoms

A

Alport syndrome - isolated hematuria (glomerulonephritis), sensory hearing loss, ocular disturbances

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61
Q

Autoantibodies against type 4 collagen (basal membrane)

Clinical symptoms

A

Goopasture syndrome

Hematurua (rapidly progressive glomerulonephritis) and hemoptysis, classically in young adult males

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62
Q

Where is collagen type 4 founded

A
  1. Basement membrane
  2. Basal lamina
  3. Lens
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63
Q

Plasma membrane structure

A

Assymetric lipid bilayer

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64
Q

Plasma membrane composition

A

Cholesterol, phospholipids, sphingolipids, glycolipids, proteins, ergosterol (fungal membrane)

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65
Q

Animal vs fungal plasma membrane

A

Fungal plasma membrane contains ergosterol

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66
Q

Bacterial vs eukaryotic plasma membranes

A

Bacterial plasma membrane lacks sterols (with some exceptions)

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68
Q

Immunohistochemical stains for intermediate filaments

A
  1. Vimentin
  2. Desmin
  3. Cytokeratin
  4. GFAP
  5. Neurofilaments
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69
Q

Vimentin stain is specific for: (cell type and identifies)

A

cell type: mesenchymal tissue (fibroblast, endothelial cells, macrophages
identifies: mesenchymal tumors (sarcomas) but also many other (enometrial ca, renal cell ca, meningiomas)

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70
Q

Desmin stain is specific for: (cell type and identifies)

A

Muscle cells

muscle tumors

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71
Q

Cytokeratin stain is specific for: (cell type and identifies)

A

Epithelial cells

eg. SCC

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72
Q

GFAP Stain is specific for: (cell type and identifies)

A

Neuroglia

Astrocytoma, GBM

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72
Q

Osteogenesis imperfecta is a genetic bone disorder also called:

A

Brittle bone disease

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73
Q

Neurofilaments stain is specific for: (cell type and identifies)

A 
Neurons
neuronal tumors (eg. neuroblastoma
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75
Q

Ostegenenis imperfecta is caused by a variety pf gene defects. Most common? genes?

A

Most common is autosomal dominant with low production of otherwise NORMAL COLLAGEN 1
genes: COL1A1 and COL1A2

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75
Q

Causes of blue sclerae in osteogenesis imperfecta

A

Due translucency of the connective tissue over the CHOROIDAL VEINS

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76
Q

Clinical manifestations of osteogenesis imperfecta

A
  1. Multiple fractures with minimal trauma (may occur during birth)
  2. Blue sclerae
  3. Hearing loss (abnormal ossicles)
  4. Dental imperfections - opalescent teeth that wear easily due to lack of dentin (dentinogenesis imperfecta)
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77
Q

Causes of hearing loss in osteogenesis imperfecta

A

Abnormal ossicles - easily fracture

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78
Q

Which disease can mimic child abuse

A

Osteogenesis imperfecta can mimic child abuse, but bruising is absent

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79
Q

Causes of dental imperfections in osteogenesis imperfecta

A

opalescent teeth that wear easily due to lack of dentin (dentinogenesis imperfecta)

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80
Q

Osteogenesis imperfecta in imaging

A
  1. Severe skeletal deformity

2. Limb shortening due to multiple fractures in a child

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81
Q

Ehlers-Danlos syndrome etiology

A

Faulty collagen synthesis

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82
Q

Most common clinical manifestations of Ehlers-Danlos syndrome

A
  1. Hyperextensible skin
  2. Tendency to bleed (easy bruising)
  3. Hypermobile joints
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83
Q

How many types of Ehlers-Danlos syndrome are exist?

A

6+ types

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84
Q

Is Ehlers-Danlos syndrome an inherited disease?

Is it severe

A

Inheritance and severity VARY

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85
Q

Is Ehlers-Danlos syndrome autosomal dominant or recessive?

A

Ehlers-Danlos syndrome can b autosomal dominant or recessive

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86
Q

Except hyoeextensible skin, tendency to blled and hypermobile joints, what else clinical manifestations can be associated with Ehlers-Danlos syndrome?

A
  1. Joint dislocation
  2. Berry aneurism
  3. Aortic aneurism
  4. Organ rupture
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87
Q

The most common type of Ehlers-Danlos syndrome

A

Hypermobility type (joint instability)

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88
Q

Which is the classical type of Ehlers-Danlos syndrome? Which collagen type of collagen is affected?

A

Joint and skin symptoms

MUTATION in collagen type 5

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89
Q

What is vascular type of Ehlers-Danlos syndrome?

Which type of collagen is affected in vascular type of Ehlers-Danlos syndrome?

A

Vascular and organ rupture

DEFICIENT type 3 collagen

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90
Q

3 types of Ehlers-Danlos syndrome and clinical manifestations

A
  1. Hypermobility type ( joint instability) most common
  2. Classical type (joint and skin symptoms) (5 collagen)
  3. Vascular type (vascular and organ rupture) (3 collagen)
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92
Q

What type of tissue does Menkes disease affect / mode of inheritance

A

Conective tissue

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92
Q

copper is necessary cofactor of which enzyme

A

Lysyl oxidase

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93
Q

Menkes disease - mechanism

A

Impaired COPPER absorption and transport due to defective Menkes protein (ATP7A) –> low activity of LYSYL OXIDASE (copper is necessary cofactor)

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94
Q

Clinical manifestations of Menkes disease:

A
  1. Brittle hair
  2. Kinky hair
  3. Growth retardation
  4. Hypotonia
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95
Q

What is lysyl oxidase?

A

Lysyl oxidase is an extracellular copper enzyme that catalyzes formation of aldehydes from lysine residues in collagen and elastin precursors.

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96
Q

What is elastin?

A

Elastin is a protein in connective tissue that is elastic and allows many tissues in the body to resume their shape after stretching or contracting.

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97
Q

Location of elastin

A
  1. Skin
  2. Lungs
  3. Elastic ligaments
  4. Vocal cords
  5. Ligamenta flava (connects vertebrae)
  6. Large arteries
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98
Q

Elastin is rich with which aminoacids and in which forms

A

PROLINE and GLYCINE and LYSINE in nonhydroxylated forms

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99
Q

Elastin is broken down by

A

Elastase

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100
Q

Elastase in normally inhibited by:

A

a1-antitrypsin

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101
Q

Elastin cross-linking takes place

What is the purpose of cross-linking

A

Extracellularly

It gives elastin its elastic properties

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102
Q

Elastin structure

A

Tropoelastin with fibrillin scaffolding

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103
Q

What is fibrillin

A

Glycoprotein that forms a sheath around elastin

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104
Q

What is ligamenta flava

A

Ligament that connects vertebrae-relaxed and stretched conformation

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105
Q

Disease caused by a defect in fibrillin

A

MARFAN

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106
Q

Diseased that can be caused by a1-antitrypsin deficiency

A

Emphysema (from excess elastase activity)

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107
Q

Pathophysiology of emphesema

A

A1-antitrypsin deficiency, resulting in excess elasetase activity

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108
Q

Wrinkles of aging are due to

A

Low collagen and elastin production

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109
Q

Microtubule shape

A

Cylindrical

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110
Q

Microtubules are cylindrical structure composed of:

A

A helical array of polymerrized heterodimeres of α and β tubulin

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111
Q

Polymerized heterodimers of microtubules are composed by

A
  1. α-tubulin

2. β-tubulin

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112
Q

Microtubules Heterodimers - GTP association

A

Each dimer has 2 GTP bound

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113
Q

Microtubule has 2 ends

A
  1. Positive end

2. Negative end

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114
Q

Microtubules are incorporated into:

A
  1. Flagella
  2. Cilia
  3. Mitotic spindle
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115
Q

Microtubule is a dynamic structure

A

Grows slowly

Collapses quickly

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116
Q

What is protofilament in microtubule

How many protfilaments in each microtubule

A

A vertical line of heterodimers

13

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117
Q

Which is the role of microtubules in transport in neurons

A

They are involved in slow axoplasmic transport transport in neurons

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118
Q

What is the role of the molecular motor proteins?

A

Molecular proteins TRANSPORT CELLULAR CARGO toward opposite ends of microtubules

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119
Q

2 molecular motor proteins

A
  1. Dynein

2. Kinesin

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120
Q

Dynein direction

A

Retrograde to microtubule (+ end to - end)

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121
Q

Kinesin direction

A

Anterograde to microtubule (- end to + end)

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122
Q

Dynein vs kinesin

A

Dynein: + to -
Kinesin: - to +

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123
Q

Drugs that act on microtubules and their clinical uses

A
  1. Mebendazole (anti-helminthic)
  2. Griseofulvin (anti-fungal)
  3. Colchicine (anti-gout)
  4. Vincristine (anti-cancer)
  5. Vinvlastine (anti-cancer)
  6. Paclitaxel (anti-cancer)
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124
Q

Anti-fungal drug that acts on microtubules

A

Griseofulvin

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126
Q

Cilia structure

A
  • 9+2 arrangement of microtubules
    the base of a cilium below the cell membrane, called the basal body condists of 9 microtubules TRIPLETS with no central micotubules
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126
Q

axonemal dynein - ATPase role:

A

It links peripheral 9 doublets and causes bending of cilium by differential sliding of tubules

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127
Q

Molecular motor protein of cilia

A

Axonemal dynein - ATPase

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128
Q

Energy of dynein and kinesin

A

ATP

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129
Q

Disease associated with cilia

A

Kartagener syndrome

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130
Q

Kartagener syndrome is also called

A

Primary ciliary dyskinesia

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131
Q

Pathophysiology of kartegener syndrome (primary ciliary dyskinesia)

A

Immotile cilia due to a dynein arm defect

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132
Q

Example of situs inversus

A

Dextrocardia (on CXR)

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133
Q

Kartagener syndrome clinical manifestations

A
  1. Male infertility
  2. Female infertility
  3. Risk for ectopic pregnancy
  4. Bronchiectasia
  5. Recurrent sinusitis
  6. Situs inversus
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135
Q

Cause of infertility in Katagener syndrome

A

male: Immotile sperm
female: Dysfunctional fallopian tube cilia

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136
Q

Cytoskeletal elements?

A

a netwrokd of protein fibers within the cytoplasm that sapports cell structure, cell and organelle moementt, and cell division

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137
Q

cytoskeletal elements - types

A
  1. microfilaments
  2. intermediate filaments
  3. microtubules
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138
Q

microfilaments - predominate function and examples

A

muscle contraction, cytokinesis

ex: actin, microvilli

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139
Q

intermediate filaments - predominate function and examples

A

maintain cell structure

ex: vimentin, desmin, cytokerain, lamins, Glial fibrillary acid proteins (GFAP), neurofillaments

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139
Q

Cells tha produce collagen

A

Fibroblasts

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140
Q

Microtubule - predominate function and examples

A

Movement, cell division

ex. cilia, flagella, mitotic spindle, axonal trafficking, centrioles

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141
Q

Synthesis of collagen

Where

A

Translation of collagen α chains (preprocollagen)

Rough endoplasmic reticulum

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142
Q

phases of collagen production and the site of them

A
  1. Synthesis (RER)
  2. Hydroxylation (RER)
  3. Glycosylation (RER)
  4. Exocytosis (from fibroblasts)
  5. Proteolytic processing ( outside fibroblasts)
  6. Cross linking ( outside fibroblasts)
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143
Q

Preprocollagen sequence

A

Usually Gly-X-Y (X and Y are proline or lysine)

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144
Q

Collagen is 1/3…

A

Glycine

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145
Q

……… content best reflects collagen synthesis?

A

Glycine

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146
Q

Hydroxylation as a part of collagen production

Where

A

Hydroxylation of specific proline and lysine residues

Rough endoplasmic reticulum

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147
Q

It is necessary for collagen hydroxylation:

A

Vitamine C

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149
Q

Vitamine C deficiency in collagen synthesis

A

Inhibits hydroxylation of collagen (Scurvy)

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149
Q

Procollagen?

A

Triple helix of 3 collagen α chains bind by hydrogen and disulfide bonds

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150
Q

Glycosylation as as a part of collagen production

Where

A

Glycosylation of pro-α-chain hydroxylysine residues and formation of procollagen via hydrogen and disulfide bonds (triple helix of 3 collagen a chain
RER

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151
Q

Procollagen bonds

A

Hydrogen and disulfide bonds

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152
Q

Problems forming triple helix (procollagen)

A

Osteogenesis imperfecta

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153
Q

Exocytosis as a part of collagen production

A

Exocytosis of procollagen into extracellular space

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154
Q

Proteolytic processing as a part of colllagen production

Where

A

Cleavage of disulfide - rich terminal regions of procollagen, transforming it into insoluble tropocollagen
Outside fibroblasts

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156
Q

Cross linking as a part of collagen production

Where

A

Covalent lysine - hydroxylysine ( cross linkage) by lysyl oxidase (copper) to make collagen fibrils. (Reinforcement of many staggerd tropocollagen molecules)

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156
Q

Collagen production pathway

A

Preprocollagen - procollagen - tropocollagen - collagen fibrils

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157
Q

Problem with cross linking of tropocollagen

A
  1. Elhers-Danlos

2. Menkes disease

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159
Q

DNA charge

Histone octamer charge

A

DNA –> Negative

Histone octamer charge –> Positive

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160
Q

Chromatin structure

A

DNA loops twice around histone octamer to form nucleosome bead

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161
Q

Nucleosome bead

A

Negatively charged DNA around positively charged histone octamer

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162
Q

Amino acids of histones

A

reach lysin and arginine

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163
Q

Types of histones

A

H1 H2A H2B H3 H4

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164
Q

Nucleosome core histones

A

H2A H2B H3 H4 (each 2 times)

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165
Q

The only histone that is not in the nucleosome core

A

H1

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166
Q

H1 location and role

A

H1 binds to nucleosome and to linker DNA thereby STABILIZING the chromatin fiber

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167
Q

DNA IN MITOSIS

A

In mitosis DNA condenses to form chromosomes

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168
Q

Cell cycle phase of chromosomes

A

Mitosis

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169
Q

Cell cycle phase of DNA and histone synthesis

A

S PHASE

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170
Q

CELL CYCLE OF HISTONE SYNTHESIS

A

S PHASE

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171
Q

Heterochromatin

A

Condensed, transcriptionally inactive, sterically inaccessible DNA

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172
Q

Euchromatin

A

Less condensed, Transcriptionally active, sterically accessible

173
Q

Transcriptionally active and inactive DNA

A

active –> Euchromatin

inactive –> Heterochromatin

174
Q

Sterically accessible and inaccessible DNA

A

accessible –> Euchromatin

inaccessible –> Heterochromatin

175
Q

Chromatin is like

A

Beads on a string

176
Q

DNA methylation at……represses transcription

A

CpG islands

177
Q

The role of methylation at CpG islands

A

Repress trancription

178
Q

Which nucleotides are methylated during DNA replication and in which strand

A

Cytosine and Adenine

Template strand

179
Q

What is the purpose of template strand cytosine and adenine methylation during DNA replication

A

Mismatch repair enzyme can then distinguish between old and new strands in prokaryotes

180
Q

How does histone chemical modification influence DNA

A
  1. Histone methylation repress DNA transcription (activate it in some cases)
  2. Histone acetylation relax DNA, allowing for trancription
181
Q

Purines vs Pyrimidines according to types and structures

A

Purines (A, G) - 2 rings

Pyrimidines (C, T, U) - 1 ring

182
Q

Thymine difference in chemical structure

A

Thymine has a METHYL

183
Q

Cytosine and uracil chemical relationship

A

Deamination of cytosine makes uracil

184
Q

Uracil found in

185
Q

Thymine found in

186
Q

Nucleotides bounds

A

Hydrogen bounds

187
Q

Nucleotides pairs and number of bonds / stronger?

A

G-C (3 H bonds)
A-T (2 H bonds)
G-C is stronger

188
Q

High G-C content –>

A

High melting temperature of DNA

189
Q

Amino acids necessary for purine synthesis

A

GAG

  1. Glycine
  2. Aspartare
  3. Glutamate
190
Q

NoucleoSide - structure

A

Base + (deoxy)ribose (sugar)

191
Q

NucleoTide - - structure

A

Base + (deoxy)ribose (sugar) + PHOSPHATE

192
Q

Phosphate is linked to nucleotide by

A

3-5 phosphodiester bond

193
Q

Besides glycine, aspartate, glutamate, which substance participate in purine synthesis

A

N10-Formyl tetrahydrofolate

194
Q

Purine base production de novo requires

A

Aspartate
Glycine
Glutamine
THF

195
Q

Purine production process

A
  1. Start with sugar (ribose 5-P) + phosphate = PRPP (phosphorybosil pyrophosphate (enzyme: PRPP synthetase)
  2. Add GAG ( to make the base) = IMP (inosinic acid)
  3. IMP - AMP or GMP (enzyme for IMP to GMP IMP dehydrogenase)
196
Q

The initial sugar for purine synthesis

A

Ribose 5 - P

197
Q

Main enzyme in purine synthesis

A

PRPP synthetase (phosphoribosyl pyrophosphate synthetase)

198
Q

Pyrimidine base production requires

199
Q

Pyrimidines synthesis process (generally)

A
  1. Make temporary base (orotic base)
  2. Add PRPP (sugar and phosphate)
  3. Base modification
200
Q

temporary base for pyrimidine synthesis

A

Orotic base

201
Q

Orotic base production

A
  1. Glutamate + CO2 + 2 ATP = carbamoyl phosphate 2 + glutamamine + 2 ADP + 2P (enzyme:carbamoyl phosphate synthetase 2)
  2. Carbamoyl phosphate + aspartate = orotic acid (enzyme:dihydroorare dehydrogenase)
202
Q

Orotic acid. Next step for pyrimidines synthesis?

A

Orotic acid+PRPP=UMP (uridine monophosphate)
UMP to UDP
UDP to dUDP (enzyme: ribonucleotide reductase)

203
Q

UDP. 2 possible next steps

A
  1. CTP

2. dUDP - dUMP - dTMP (thymidylate synthetase)

204
Q

DUMP TO DTMP

A

dUMP + N5N10 Methylene THF=dTMP +DHF (enzyme: thymidylate synthetase)

205
Q

THF cycle

A

N5N10 Methylene THF - DHF (thymidylate synthase) - THF (dihydrofolate reductase) - THF - N5N10 Methylene THF

206
Q

Deoxyribonucleotides synthesis

A

Ribonucleotides are synthesized first and are convertes to deoxyribonucleotides by ribonucleotide reductase

207
Q

Enzyme: ribonucleotide reductase

A

Convert ribonucleotides to deoxyribonucleotides

208
Q

Dihydroorate dehydrogenase inhibitor (explain)

A

Leflunomide (Carbamoyl phosphate to orotic acid)

209
Q

Ribonucleotide reductase inhibitor (explain)

A

Hydroxyuria (UDP to dUDP)

210
Q

IMP dehydrogenase inhibitor (explain)

A

Mycophenolate
Ribavirin
(IMP to UMP)

211
Q

Thymidylate synthase inhibitor (explain)

A

5-fluorouracil (5-FU) –> forms 5-F-dUMP

dUMP to dTMP

212
Q

PRPP to IMP inhibitor

A

6-mercaptopurine (6-MP)

Azathioprine (prodrug of 6-MP)

213
Q

Dehydrofolate reductase inhibitor in humans, bacteria and protozoa

A

Human - methotrexate
Bacteria - trimethoprim
Protozoa - pyrimethamine

214
Q

Genetic code is unambiguous

A

Each codon specifies 1 amino acid

215
Q

Genetic code is degenerate/redundant

A

Most amino acids are coded by multiple codons

Exceptions: methionine, tryptophan

216
Q

Amino acids that coded by one codon (and which codon)

A

Methionine - AUG

Tryptophan - UGG

217
Q

Genetic code is universal

A

It conserved throughout evolution

Exception in humans: mitochondria

218
Q

Exceptions of universal genetic code in human

A

Mitochondria

219
Q

Genetic code is comma-less, non overlapping

A

Aread from fixed starting point as a continuous sequence of bases
Exceptions:some virus

220
Q

Exceptions of comma-less, nonoverlapping gemetic code

A

Some virus

221
Q

Genetic codes features

A
  1. Unambiguous
  2. Degenerate/redundant
  3. Comma-less, nonoverlapping
  4. Universal
222
Q

Carbamoyl phosphate is involved in 2 metabolic pathways

A
  1. De novo pyrimidine synthesis

2. Urea cycle

223
Q

IMP to urine - pathways and enzymes (and combinations with other pathways)

A
  • IMP –> Inosine –> Hypoxanthine (XO) –> Xanthine (XO) –> Uric acid –> urine
  • IMP AMP
  • Adenosine –> Inosine (ADA)
  • Guanine –> xanthine
  • Hypoxanthine + PRPP –> IMP (HGRTT
224
Q

HGPRT? APRT? meaning and action

A 
Hypoxanthine guanine phosphoribosyltransferase: 
- Hypoxanthine + PRPP to IMP
- Guanine + PRPP to GMP 
Adenine phosphoribosyltransferase: 
- adenine + PRPP to AMP
225
Q

Purine salvage deficiencies - Adenine

A

Nucleoic acid –> AMP

Adenine + PRPP –> AMP (APRT)

226
Q

Purine salvage deficiencies - guanine

A

Nucleic acid –> GMP –> Gianosine –> Guanine –> Xanthine

Guanine + PRPP (HGPRT) –> GMP

227
Q

ways of IMP synthesis

A
  1. de novo (Ribose-5-P via PRPP synthetase)
  2. Hypoxanthine + PRPP to IMP (HGPRT_
    • IMP AMP
228
Q

Adenosine deaminase deficiency pathophysiology

A

ADA is required for degration of adnononisne and deoxyoadenosine (nucleosides) (to make them inosine) –> increased dATP –> toxicity in lymphocytes –> Severe combined immunodeficiency (SCID)

229
Q

Is adenosine deaminase deficiency inheritable?

A

it is one of the MCC AR SCIDs

230
Q

Adenosine deaminase (ADA) role

A

Adenosine to inosine (both nucleosides)

231
Q

Lesch-Nyhan syndrome problem

A

Defective purine salvage due to HGRPT) deficiency or absent which convert Hypoxanthine to IMP and guanine to GMP

232
Q

Lesch-nyhan syndrome results in:

Inheritable?

A

Excess uric acid production and de novo purine synthesis

X linked recessive

233
Q

Lesch-nyhan syndrome treatment

A

Allopurinol

Febuxostat (2nd line)

234
Q

Lech-nyhan syndrome clinical manifestations:

A 
Mnemonic HGPRT
Hyperuricemia
Gout
Pissed off (aggression, self-mutilation)
Retardation
DysTonia
235
Q

Which is more complex, eukaryotic or prokaryotic DNA replication?

A

Eukaryotic replication is more compex but uses many analogous enzymes

236
Q

In both, prokaryotes and eukaryotes, DNA replication is ….. and involves both ……and …..synthesis

A

In both eukaryotes and prokaryotes, DNA replication is SEMICONSERVATIVE and involves both CONTINUOUS and DISCONTINUOUS (OKAZAKI FRAGMENT) synthesis

237
Q

Okazaki synthesis

A

Discontinious synthesis

238
Q

Origin of replication

A

Particular consensus sequence of base pairs in genome where DNA replication begins
Single in prokaryotes
Multiple in eukaryotes

239
Q

Number of replication origin

A

Single in prokaryotes

Multiple in eukaryotes

240
Q

Replication fork

A

Y-shaped region along DNA template where leading and lagging strands are synthesized

241
Q

Helicase

A

Unwinds DNA template at replication fork

242
Q

Enzyme responsible for DNA template unwinding at replication fork

A

DNA helicase

243
Q

Single-stranded binding proteins (DNA) - function

A

Prevents strands from reannealing

244
Q

topoisomerase inhibitors (and action)

A

fluoroquinolones: gyrase (prokaryotic topoisomerase 2) and topoisomerase 4
etoposide, tenoposide –> topoisomerase 2
Irinotecan, topotecan –> topoisomerase 1

245
Q

Prokaryotic topoisomerase type 2 is also called

246
Q

DNA topoisomerases

A

Create a single or double stranded break in the helix to add or remove supercoils

247
Q

Primase (dna)

A

Makes an RNA primer on which DNA polymerase 3 can initiate replication

248
Q

Where is DNA polymerase 3 founded

A

Only in prokaryotes

249
Q

Polymerase type 3 function

A
  1. Elongates leading strand by adding deoxynucleotides to the 3 end
  2. Elongates lagging strand until it reaches primer of preceding fragment
  3. 3 to 5 exonuclease activity proofreads each added nucleotide
250
Q

Enzyme with 5 to 3 synthesis and profreads with 3 to 5 exonuclease

A

DNA Polymerase type 3

251
Q

DNA polymerase type 1 - action / found

A

Degrades RNA primer (5 to 3 exonuclease)replace it with DNA (5 to 3 elongation and 3 to 5 exonuclease activity proofreading)
Only prokaryotes

252
Q

DNA polymerase 1 vs DNA polymerase 3

A

They have the same function but DNA polymerase 1 also excise RNA primer with 5 to 3 exonuclease

253
Q

DNA ligase

A

Formation of phosphodiester bond with a strand of double -stranded DNA (ex joints Okazaki fragments)

254
Q

Telomerase

A

RNA dependent DNA polymerase that adds DNA to 3 ends of chromosome to avoid loss of genetic material with every duplication

255
Q

Enzyme that participate in DNA replication

A
  1. Helicase
  2. Single -stranded binding proteins
  3. DNA topoisomerase
  4. Primase
  5. DNA polymerase 3 (prokaryotes)
  6. DNA polymerase 1 (prokaryotes)
  7. DNA ligase
  8. Telomerase (eukariotes)
256
Q

type of mutations in DNA

A
  1. silent 2. Missense 3. Nonsense

4. Frameshift 5. Splice site

257
Q

Silent mutation

A

Nucleotide substitution but codes for same amino acid

Often 3rd position of codon (tRNA) wobble

258
Q

Missense mutation (and example)

A

Nucleotide substitution resultin in chamged aminacid
If new amino acid is similar to chemical structure—> conservative
example Sicke cell disease

259
Q

Conservative missense mutation

A

If new amino acid is similar in chemical structure

example: Sicke cell disease

260
Q

Nonsense mutation

A

Nucleotide substitution resulting in early stop codon –> nonfunctional protein

261
Q

Frameshift mutation

A

Deletion or insertion of a number of nucleotides not divisible by 3 resulting in misreading of all nucleotides downstream, usually resulting in a trancated, NONFUNCTIONAL PROTEIN

262
Q

Frameshoft mutation - example

splice site mutation - example

A

Frame: 1. Duchenne muscular dystrophy 2. Tay Sachs disease
Splice: cancers, dementia, epilepsy, some types of β-thalassemia

263
Q

splice site mutation?

A

mutation at a splice site –> retained intron tn the mRNA –> protein with imparaid or altered function

264
Q

Severity of mutations (in order) (from most severe to less

A

Frameshift –> nonsense –> mssense –> silent

265
Q

Transition? (For silent, missense, nonsesne mutation)

A

Purine to purine or pyrimidine to pyrimidine

266
Q

Transversion? (For silent, missense, nonsesne mutation)

A

Purine to pyrimidine

Or pyrimidine to purine

267
Q

DNA repair - ways

A
  1. Nucleotide excision repair (single strand)
  2. Base excision repair (single strand)
  3. Mismatch repair (single strand)
  4. Nonhomologous and joining (double strand)
268
Q

Nucleotide excision repair?

A

Specific endonucleases release the oligonucleptide-containing damaged bases –> DNA polymerase and ligase fills and reseal the gap –>

269
Q

Defective in xeroderma pigmentosum

A

Nucleotide excision repair (single strand) –> UV causes pyrimidine dimers

270
Q

What is the problem in dna after ultraviolet exposure

A

Pyrimidine dimers

271
Q

What type of lessions does nucleotide excision repair system repair

A

It repairs BYLKY helix - distorting lesioms

272
Q

nucleotide excision repair system - acts during

273
Q

Important in repair of spontaneous/toxic deamination

Acts during

A

Bade excision system

All cycle

274
Q

Base excision repair system steps

A
  1. Glycosylase recognized altered base and creates apurinic/ apyrimidinic site (AP site)
  2. One or more nucleotides are removed by AP-endonuclease, wchich cleaves 5 end.
  3. Lyase cleaves 3 end
  4. DNA polymerase β fills the gap
  5. DNA ligase seals the gap
  6. DNA polymerase fills the gap
275
Q

Base excision repair system enzymes

A
  1. Glycosylase
  2. AP exonclease
  3. Lyase
  4. DNA polymerase β
  5. DNA ligase
276
Q

Defective in hereditary nonpolyposis colorectal cancer (HNPCC)

A

mismatch repair system

277
Q

Mismatch repair system

Acts during

A

Newly synthesized strand is recognized, ,ismatched nucleotides are removed, and the gap is filled and realised
G2

278
Q

The first step of mismatch repair system

A

Recognizes newly synthesized strand

279
Q

defective in Nonhomologous and joining repair system - example

A
  1. ataxia telengiectasis

2. fanconi anemia

280
Q

Nonhomologous end joining repair system

A

Brings together 2 ends of DNA fragments to repair. Double stranded breaks. No requirement for homologous

281
Q

Nonhomologous end joining repair system - disadvantage

A

some DNA may be lost

282
Q

Double stranded DNA repair system

A

Nonhomologous end joining

283
Q

Single strand DNA repair system

A
  1. Nucleotide excision repair
  2. Base excision repair
  3. Mismatch repair
284
Q

DNA synthesis direction
RNA synthesis direction
protein synthesis direction

A

RNA/DNA 5 to 3

PROTEIN N-terminus to C-terminus

285
Q

Energy source for bond in RNA/DNA synthesis

A

The 5 end of incoming nucleotide bears the triphosphate

286
Q

mRNA read direction

287
Q

DNA chain termination drugs mechanism of action

A

They have a modified 3 OH, preventing addition to the next nucleotide

288
Q

The triphosphate bond is the target of which enzyme

A

3hydroxyl attack

289
Q

Start codon

A

AUG

Rarely GUG

290
Q

Start codon - eukaryotes - amino acids

A

Methionine, which may be removed before translation is completed

291
Q

Start codon - prokaryotes - amino acids

A

Codes for formylmethionine (f-met)

292
Q

mRNA stop codons

A

UGA (U Go Away)
UAA (U Are Away)
UAG (U Are Gone)

293
Q

2 strands of a gene

A
  1. Template strand

2. Sense/coding strand

294
Q

Promoter - definition

A

Site of RNA polymerase II and multiple other transcription factors bind to DNA upstream from gene locus

295
Q

Promoter sequence

A

AT - rich upstream sequence with TATA and CAAT boxes

296
Q

TATA box

CAAT box

A

Template strand:ATATTA, GTTA

Sense/coding strand: TATAAT, CAAT

297
Q

Promoter mutation

A

Dramatic decreasing in level of gene trancription

298
Q

Silencer

A

Site where negative regulators (repressors) bind

299
Q

Enhancer

A

Stretch of DNA that alters gene expression by binding transcription factors

300
Q

Enhancers and silencers location

A

Close to, far from or even within (in an intron) the gene whose expression it regulates

301
Q

Regulation of gene expression DNA sites

A
  1. Promoter
  2. Enhancer
  3. Silencer
302
Q

Eukaryotes RNA polymerase

A
  1. RNA polymerase type 1 - rRNA
  2. RNA polymerase type 2 - mRNA
  3. RNA polymerase type 3 - tRNA (5S rRNA)
    NUMBERED IN THE SAME ORDER THAT THEIR PRODUCTS ARE USED IN PROTEIN SYNTESIS
303
Q

Prokaryotes RNA polymerase

A

1 RNA polymerase makes all 3 kinds of RNA (Multisubunit complex)

304
Q

Most numerous RNA
largest RNA
smallest RNA

A

most numerous: rRNA

largest: mRNA
smallest: tRNA

305
Q

a-amantin (where is founded, mechanism of action, clinical manifestations)

A 
Amanita phalloides (death cap mashrooms), 
It inhibits RNA polymerase type 2
Causes severe hepatotoxicitu if ingested
306
Q

Amanita phalloides (death cap mushrooms) contain

307
Q

Rifampin - mechanism of action

A

inhibits RNA polymerase in prokaryotes

308
Q

Actinomycin D mechanism of action

A

inhibits RNA plymerase in both prokaryotikes and eukariotes

309
Q

Enzyme that opens DNA at promoter site

A

RNA polymerase type 2

310
Q

RNA polymerase vs DNA polymerase according proofreading function and chain initiation

A

RNA POLYMERASE HAS NO PROOFREADING FUNCTION BUT IT can initiate chains

311
Q

hnRNA

A

Heterogenous nuclear RNA

312
Q

Heterogenous nuclear RNA (hnRNA). (eukaryotes)???

A

It is the initial transcript. It is then modified and becomes mRNA

314
Q

Capping of 5 end (eukaryotes)

A

Addition of 7-methylguanosine gap

315
Q

Polyadenylation of 3 end
Enzyme. (eukaryotes)
SIGNAL

A

Addition of 200 at 3 end
Poly A- polymerase (does not require template)
AAUAAA

316
Q

AAUAAA (eukaryotes)

A

Polyadenylation signal

317
Q

Location of mRNA translation (eukaryotes)

A

Cytosol (mRNA is transported out of the nucleous into cytosol)

318
Q

P bodies function and structure (eukaryotes)

A
  • distinct foci within the cytoplasm of the eukaryotic cell
  • contain Exonucleases, decapping enzymes, microRNA
  • mRNA control
  • mRNA is may be stored their for future translation
320
Q

Splicing of pre-mRNA

A
  1. Primary transcript combine with small nuclear ribonucleoproteins (SnRNPs) and other proteins to form spliceosome
  2. Lariat - shaped (looped) intermediate is generated
  3. Lariat is released to precisely remove intron and join 2 exons
331
Q

In eukaryotes, tRNA / mRNA rRNA is synthesized by

A

tRNA –> RNA polymerase type 3
mRNA –> RNA polymerase type 2
rRNA –> RNA polymerase type 1

332
Q

From DNA to protein (the name of the processes

A

DNA –> hnRNA (transcription) –> mRNA (splicing) –> proteins (translation)

335
Q

Shape of secondary structure of tRNA

A

Cloverleaf: anticodon end is opposite 3-aminoacyl end

337
Q

CCA of tRNA

A
  • CCA at 3 end along with a high percentage of chemically modified bases
  • both eukariotic and prokaryotic
  • 3 - ACC
  • contently bound aminoacid
340
Q

T arm of tRNA

A

Contains ΤΨC (ribothymidine, pseudouridine, cytidine) sequence necessary for tRNA-ribosome binding

341
Q

TΨC sequence of tRNA

A

ribothymidine, pseudouridine, cytidine

343
Q

Acceptor stem of tRNA

A

3-ACC-5 - OH is the amino amino acid acceptor side + more nucleotides

344
Q

Sequence of tRNA amino acid acceptor site (acceptor site)

A

3-ACC-5 - OH

346
Q

Energy of aminoacyl tRNA (formation of tRNA binded with aminoacid)

347
Q

Amino acid matchmaker of tRNA

A

Aminoacyl-tRNA synthetase (1 per amino acid). It also scrutinizes amino acid before and after it binds to tRNA. If incorrect, bond is hydrolized

355
Q

Posttanslational modifications types

A
  1. Trimming

2. Covalent alternations

356
Q

Triming (type of posttranslational) modification

example

A

Removal of N- or C- propeptides from zymogen (inactivate enzyme precursor) to generate mature proteins
example: trypsinogen –> tripsin

359
Q

3 steps of protein synthesis

A
  1. Initiation
  2. Elongation
  3. Termination
362
Q

Protein synthesis initiation prosses

A

Initiated by GTP hydrolysis. Initiation factors (eukaryotic IF) help assemble the 40s ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60s subunit assemble with the complex (initiation complex)

363
Q

3 site of 60s rRNA elongation

A

APE
A site = incoming aminoacyl-tRNA (except for initiator methinine)
P site = accommodates growing peptide
E site= holds empty tRNA as it exits

366
Q

Elongation of protein synthesis

A
  1. Aminoacyl - tRNA binds tomA site (except initiator methionine)
  2. rRNA (ribozome) catalizes peptide bond formation, transfer growing polypeptide to amino acid in A site
  3. Ribosomes advances 3 nucleotides toward 3 end of mRNA , moving peptidyl tRNA to P site (traslocation)
368
Q

Polymerase chain reaction (PCR)? (definition, purpose)

A

Molecular biology laboratory procedure used to AMPLIFY A DESIRED FRAGMENT OF DNA. Useful as a diagnostic tool

369
Q

In clinical practice, PCR is useful as a: (and examples)

A

Diagnostic tool (ex. Neonatal HIV, herpes encephalitis)

370
Q

Steps of Polymerase chain reaction (PCR) and temperature

A
  1. Denaturation –> 95
  2. Annealing –> 55
  3. Elongation –> 72
    These steps are repeated multiple times for DNA sequence amplification
371
Q

Denaturation (PCR)

A

DNA is denaturated by heating to generate 2 separate strands (95 C)

372
Q

Annealing (PCR)

A

During cooling, excess DNA primers anneal to a specific sequence on each strand to be amplified
(55 C)

373
Q

Elongation (PCR)

A

Heat stable DNA polymerase replicates the DHA sequence following each primer (72 C)

374
Q

PCR - after the 3 steps

A

Agarose gel electrophoresis

376
Q

Bloatting procedures

A
  1. Southern blot
  2. Nothern blot
  3. Western blot
  4. Southwestern blot
378
Q

The following processes occur the nucleus following transcription:
(eukaryotes)

A
  1. Capping of 5 end
  2. Polyadenylation of 3 end
  3. Splicing out of introns

CAPPES, TAILED AND SPLICED TRANSCRIPT IS CALLED mRNA

379
Q

Nothern blot is useful for:

A

mRNA evels, reflective of gene expression

384
Q

mRNA quality control occurs at (eukaryotes)

A

Cytoplasmatic P - bodies

386
Q

Splicome

A

Primary transcript combined with snRNP and other proteins

387
Q

Antibodies against spliceosomal snRNPs (anti Smith)

A

Highly specific for SLE

388
Q

Anti-Smith

A

Antibodies against spliceosomal snRNP (highly specific for lupus)

389
Q

SLE highly specific antibodies

A

Anti - Smith (antibodies against splisocoemal snRNP)

390
Q

Mixed connective tissue antibodies

A

Anti - u1 antibodies

391
Q

Major elisa variations

A
  1. direct
  2. sandwich (indirect)
  3. competitive
392
Q

Anti-U1 RNP antibodies

A

Mixed commective tisseu disease

393
Q

Exons

A

Contain the actual genetic information coding for protein

394
Q

Introns

A

Intervening noncoding segments of DNA

395
Q

Alternative splicing

A

Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins

396
Q

Abnormal splicing are implicates in

A
  1. Oncogenesis

2. Many genetic disorder (β-thalassemia)

397
Q

Fluorescence in situ hybridization (FISH)

A

Fluorescent DNA or RNA probe binds to specific gene site of interest on chromosomes. Used for specific localization of genes and direct visualization of anomalies (e.g. Microdeletions) at molecular level (when deletion is too small to be visualized by karyotype)

399
Q

FISH is used to detect (explain)

A
  1. microdeletion: no florescence on a chromosome compared to florescence at the same locus on the 2nd copy of that chromosome
  2. Tranocation: florescence outside the original chromosome
  3. Duplication: extrasite of florescence on one chromosome relative to its homologous chromosome
400
Q

Prokaryotic RNA polymerase

A

1 RNA polymerase is a multisubunit complex that makes all 3 kinds of RNA

401
Q

Number of nucleotides in tRNA

403
Q

Transgenic strategies of gene into mouse genome involve

A
  1. Random insertion of gene into mouse

2. Targeted insertion or deletion of gene through homologous recombination with mouse gene

404
Q

Where is tRNA anticodon end

A

It is opposite 3 aminoacyl end

406
Q

Where is the aminoacid on the tRNA

A

Is covalently bound to the 3 end of tRNA

407
Q

3 tRNA areas

A
  1. T arm
  2. D arm
  3. Acceptor stem
410
Q

Cre - lox system

A

Can inducibly manipulate genes at specific developmental points (e.g. to study a gene whose deletion cause embryonic death)

411
Q

tRNA TΨC function

A

Necessary for tRNA - ribosome binding

414
Q

D-arm of tRNA

A

It contains dihydrouracil residues necessary for tRNA recognitiom by the correct aminoacyl-tRNA synthetase

417
Q

Introns sequence

A

P-GU-A-AG

P binds with A to form the loop

418
Q

How many different aminoacyl-tRNA does exist

A

One per amino acid

419
Q

What if amino acid that binded to tRNA is incorrect

A

Bond is hydrolyzed. If not hydrolyzed, trna reads usual codon, vut inserts wrong amino acid

420
Q

Peptide bind energy

A

The amino acid tRNA bond has energy for formation of peptide bond

421
Q

Responsible for accuracy of amino acid selection

A
  1. Aminoacyl-tRNA synthetase

2. Binding of charged tRNA to the codon

422
Q

tRNA wobble

A

Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the third position may code for the same tRNA/amino acid ( as a result of degeneracy of genetic codes

423
Q

Chaperone proteins

A

Intracellular protein involved in facilitating and/or maintaining protein folding

424
Q

Champeron proteins in yeast

A

Some are heat shock proteins (ex Hsp60) that are expressed at high temperatures to prevent protein denaturing/misfolding

427
Q

Covalent alternations (type of posttranslational modification)

A

Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination

428
Q

Ribosomes

A

Eukaryotes: 40s + 60s–>80s

Prokaryotes 30s+50s–>70s

430
Q

tRNA actives energy

A
  1. Charging (activation) - ATP
  2. Gripping (initiation of protein synthesis) - GTP
  3. Ribosomes translocation - GTP
431
Q

Protein synthesis is initiated by

A

GTP hydrolysis

434
Q

Enzyme that catalizes peptide bond formation

How

A

Ribozome (rRNA)

It transfers growing polypeptide to amino acid A site

435
Q

Ribosome translocation

A

Ribosomes advances 3 nucleotides toward 3 end of mRNA, moving peptidyl tRNA to P site

437
Q

Termination of protein synthesis

A

Stop codon is recognized by release factor and completed polypeptide is released from ribosome

445
Q

Agarose gel electrophoresis

A

Used for size separation of PCR products (smaller molecules travel further). Compared against DNA ladder

447
Q

Southern blot steps

A
  1. DNA sample is enzymatically cleaved into smaller pieces
  2. Electrophoresed on a gel
  3. Transferred to a filter
  4. Soaked in a denaturant
  5. Exposed to a radiolabeled DNA probe that recognizes and anneals to its complementary strand
  6. Double stranded piece of DNA is visualized when the filter is exposed to film
448
Q

Nothern blot

A

Similar to southern blot, except that an RNA sample is electrophoresed.

450
Q

Method for studying mRNA levels

A

Nothern blot

451
Q

Southern vs nothern blot

A

In nothern blot, RNA sample is electrophoresed

In southern blot, DNA sample is electrophoresed

452
Q

Western blot steps

A
  1. Sample protein is separated via gel electrophoresis
  2. Transferred to a filter
  3. Labeled antibody is used to bind to relevant protein
453
Q

Western blot is used for:

A

Confirmatory test fir HIV after + ELISA

454
Q

western vs southern vs nothern blot difference according samples

A

Southern=DNA
Nothern=RNA
Western=protein

455
Q

Southwestern blot

A

Identifies DNA-binging proteins (e.g. transcription factors) using labeled oligonucleotide probes

456
Q

Karyotiping (method)

A

A process in which METAPHASE CHROMOSOMES ARE STAINED, ORDERED AND NUMBERED

457
Q

In karyotypes, we observe

A
  1. Morphology
  2. Size
  3. Arm-length ratio
  4. Banding pattern
458
Q

Karyotypes can be perform on a sample of

A
  1. Blood
  2. Bone marrow
  3. Amniotic fluid
  4. Placental tissue
459
Q

Karyotyping is used to diagnose

A

CHROMOSOMAL IMBALANCE (e.g. Autosomal trisomies, sex chromosomes disorder)

460
Q

Enzyme - linked immunosorbent assay(ELISA) is used to detect

A

The presence of of either a specific antigen (direct) or a specific antibody (indirect) in a patient’s blood sample

461
Q

Linked immunosorbent assay - direct

A

Uses a test antibody to see if a specific antigen is present in the patient’s blood. A secondary antibody coupled to a color- generating enzyme is added to detect the antigen

462
Q

Linked immunosorbent assay(ELISA) - indirect

A

Uses a test antigen to see if a specific antibody is present in the patients blood. A secondary antibody coupled to a color- generating enzyme is added to detect the antigen

463
Q

ELYSA + result

A

If the target substance is present in the sample, the test solution will have an intense color reaction

464
Q

ELYSA is used in many laboratories to determine:

A

Whether a particular antibody (e.g. anti-HIV) is oresent in a patient’s sample

465
Q

ELISA sensitivity and specificity

A

Both approach 100%, but both false-postive and false-negative results occur

467
Q

When used fluorescence in situ hybridization instead of karyotype for direct visualization of anomalies

A

When deletion is too small to be visualized by karyotype

468
Q

FISH signal

A

Fluorescense=gene is present

No fluorescence=gene has been deleted

469
Q

Cloning

A

It is the production of a recombination DNA molecule that is self perpetuating

470
Q

Cloning methods

A
  1. Isolate eukaryotic mRNA (post-RNA processing steps) of interest
  2. Expose mRNA to reverse transcriptase to produse cDNA (lacks introns)
  3. Insert cDNA fragments into bacterial plasmids containing antibiotic resistance genes
  4. Transform recombination plasmid into bacteria
  5. Surviving bacteria on antibiotic medium produce cDNA
471
Q

Knock out

A

Removing a gene

472
Q

Knock in

A

Inserting a gene

473
Q

RNAi

A

RNA interference

474
Q

RNA interference

A

dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected into human cells, dsRNA separates and promote degradation of target mRNA, “knocking down” gene exression

475
Q

RNA interference structure before transfected into human cells

A

dsRNA complementary to the mRNA sequence of interest

476
Q

RNA interference structure in human cell

A

dsRNA separates and promotes degradation of target mRNA

477
Q

Microarrays materials

A

Thousands of nuclei acid sequences are arranged in grip on glass or silicon

478
Q

Microarrays concept

A

DNA or RNA probes are hybridized to the chip, and a scanner detects the relative amounts of complementary binding

479
Q

Microarrays used to:

A

Profile gene expression levels of thousands of gene simultaneously to study certain disease and treatment

480
Q

Microarrays are able to detect:

A

Single nucleotide polymorphism (SNPs) and copy number variations (CMV) for a variety of applications including genotyping, clinical genetic testing, forensic analysis, cancer mutation, genetic linkage analysis

481
Q

Microarrays are able to detect SNPs and CNVs for a variety of applications including

A
  1. Genotyping
  2. Clinical genetic testing
  3. Forensic analysis
  4. Cancer mutation
  5. Genetic linkage analysis
482
Q

Termination signal of an eukaryotic gene

A

5-AATAAA-3
3-TTATTT-5
It is the same with the adenylation signal

483
Q

flow cytometry is laboratory technique to assess

A

size, granularity, and protein expression (immunophenotype) of individual cell in a sample

484
Q

flow cytometry comonly used in

A

workup of hematologuc abnosmalities (eg. paroxysmal noctural hemoglobinuria, fetal RBCs in mother’s blood) and immunodeficiencies (CD4 cell count in HIV)

485
Q

flow cytometry - mechanism

A

cells are tagged with antibodies specific to surface or intracellular proteins –> antibodies are then tagged with a unigue fluorescent dye –> sample is analyzed one cell at a time by focusing a laser on the cell and measuring light scatter and intensity of fluorescense –> data are plotted either as histogram (one measure) or scatter plot (any 2 measures)

486
Q

Lac operon is a classic example of

A

genetic response to an environmental change

487
Q

Glucose is the preferred metabolic substrate in E.coli. When is absent –>

A

if lactose is available –> the lac operon is activated to lactose metabolism

488
Q

lac operon - mechanism of shift

A

low glucose –> increased adenylate cyclase –> incresaed cAMP –> activation of catabolic activator protein (CAP –> increased transcription
high lactose –> unbinds repressor protein from repressor / operator site –> increased transcription (alolactose is the real binding)

489
Q

genes of Lac operon

A
  1. LacZ
  2. LacY
  3. LacA
490
Q

lac operon - low glucose / lac available?

A

strongly expressed

491
Q

lac operon - high glucose / lactose unavailable

A

not expressed

492
Q

lac operon - low glucose / lactose unavailable

A

not expressed

493
Q

lac operon - high glucose, lactose available

A

very low (basal) expression)

Biochemistry FA (16 decks)

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