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P1: Ben & Maytee Fisch College of Pharmacy > Biochem Final > Flashcards

Biochem Final Flashcards

Cumulative

1
Q

Wk7D2: The citric acid cycle is one source for providing substrates for the conversion of amino acids.

True/False

A

True

Substrates: alpha-ketoglutarate and oxaloacetate

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2
Q

Wk7D2: Amino acids can be converted to another amino acid by transamination of an alpha keto acid.

True/False

A

True

  • not a redox reaction
  • displacement of amino acid
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3
Q

Wk7D2: Amino acids can be used to produced?

a) carbohydrate
b) lipid
c) other amino acid
d) energy
e) all of the above

A

d) All of the above

  • TCA Cycle/Citric Acid Cycle
  • vitamins and minerals are not produced in the body (essential aa)
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4
Q

Wk7D2: All amino acids can be synthesized de novo or from scratch in a human body as need.

True/False

A

False

  • acquired through diet (essential AA)
  • synthesized in body (nonessential AA)
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5
Q

Wk7D2: When the amino group is removed, it is in what form and where does it go?

A

Ammonia is formed and is excreted through the urine

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6
Q

Wk7D2: How are amino acids needed differently in the body?

A
  • precursors for protein synthesis

* can be oxidized to yield energy for ATP synthesis

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7
Q

Wk7D2: Which ones can be synthesized in the body?

A

Glutamate and glutamine are 2 of the most important metabolic amino acids in the body; they serve as reservoirs of nitrogen and as the carbon skeletons for the TCA cycle intermediate, alpha-ketoglutarate

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8
Q

Wk7D2: How are amino acids classified metabolically?

A

nonessential and essential

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9
Q

Wk7D2: Name some nonessential amino acids

A 
Alanine
Asparagine
Aspartate
Cysteine
Glutamine
Glycine
Proline
Serine
Tyrosine
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10
Q

Wk7D2: Name some essential amino acid

A 
Arginine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
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11
Q

Wk7D2: What are the 3 categories that amino acids fall in?

A

Glucogenic
Ketogenic
Glucogenic and Ketogenic

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12
Q

Wk7D2: Which group give rise to a net production of pyruvate or TCA cycle intermediates: alpha-ketoglutarate and oxaloacetate?

A

Glucogenic

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13
Q

Wk7D2: Which group give rise only to acetyl-CoA or acetoacetyl-CoA?

A

Ketogenic

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14
Q

Wk7D2: Lysine and leucine are solely falls under what type of amino acid category?

A

Ketogenic

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15
Q

Wk7D2: Which group give rise to both glucose and fatty acid precursors?

A

Glutogenic and ketogenic

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16
Q

Wk7D2: Isoleucine, phenylalanine, threonine, tryptophan and tyrosine fall under which category of amino acid?

A

Glutogenic and ketogenic

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17
Q

Wk7D2: In aspartate asparagine metabolism what enzyme is important in interconversion?

A

Asparagine synthase: catalyze the conversion of aspartate to asparagine

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18
Q

Wk7D2: How can amino acids produce glucose?

A

Gluconeogenesic pathway converts pyruvate, lactate, glycerol and amino acids (alanine and glutamine) into glucose

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19
Q

Wk7D2: What is transamination used for?

A

plays a role in synthesis and breakdown of amino acids

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20
Q

Wk7D2: What is deamination?

A

removal of an amino group from an amino acid to other compound

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21
Q

Wk7D2: What are 3 mechanisms to synthesize non-essential amino acids?

A

1) Transamination via transaminases/aminotransferases
2) Incorporation of free ammonia into existing AA
(glutamate + NH3 –> glutamine via glutamine synthase)
3) Modification of carbon skeleton of existing AA

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22
Q

Wk8D2: The development of gout is due to precipitation of uric acid crystals in the joint.

True/False

A

True

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23
Q

Wk8D2: Individual nucleotides must be synthesized individually because there is no interconversion possible.

True/False

A

False

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24
Q

Wk8D2: In purine biosynthesis of an amino acid is used in the pathway.

True/False

A

True

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25
Q

Wk8D2: The de novo synthesis of nucleotides and the salvage pathway are the same pathway.

True/False

A

False

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26
Q

Wk8D2: Since gout is a disease caused by nucleotide metabolism and the accumulation of uric acids in the joint, what tissue would be most likely to exaggerate the symptoms by ingestion?

a) muscle tissue low in cell number but high in extracellular matrix
b) organ meat or tissue high in cell number
c) blood sausage made from RBC
d) celery salary
e) nuts

A

b) organ meat or tissue high in cell number

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27
Q

Wk8D2: How is nucleic metabolism involved in the disease gout?

A

uric acid comes from purine metabolism

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28
Q

Wk8D2: Uric acid comes from what part of metabolism?

a) Base
b) Sugar
c) Triphosphate

A

a) Base

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29
Q

Wk8D2: What would be some reasons why uric acid would reach such high levels?

A
  • Reduction of uric acid = overproduction

* not being excreted properly by the kidneys

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30
Q

Wk8D2: What are common drugs used to treat gout?

A

Allopurinol
Colchine
Uloric
NSAIDs (if not bad enough to medicate)

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31
Q

Wk8D2: What carbohydrate is used and where does it come into the synthesis pathway?

A
  • Ribose is phosphorylated at the beginning of the pathway

* AA provide nitrogen for bases

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32
Q

Wk8D2: What other building blocks are used in the synthesis?

A
  • AA close the ring of the structure and provide the amino group
  • Vitamin: folate and niacin
  • ATP
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33
Q

Wk9D1: Arachidonic acid is used in the production of leukotrienes.

True/False

A

True

arachidonic acids is a long chain (20 C) fatty acid; more than one bond; unsaturated; carboxylic group on an end of the chain

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34
Q

Wk9D1: What are two ways we can get a substrate as an enzyme?

A
  • Produce it ourselves –> fatty acid

* Diet

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35
Q

Wk9D1: What is the richest fatty acid place in our body?

A

lipid membrane

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36
Q

Wk9D1: The best treatment for a fever would be:

a) Steroids
b) Antibiotics
c) Drinking water
d) Drinking alcohol
e) NSAIDs

A

e) NSAIDs

* inhibits COX-1 and COX-2

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37
Q

Wk9D1: What is the temperature that is clinically considered as a fever?

A

100.4F or 38C

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38
Q

Wk9D1: The organ/tissues in the body which are responsible for acting as the thermostat to regulate and maintain your body temperature?

a) Brain
b) Liver
c) Skin
d) Hypothalamus
e) Lungs
f) Muscles

A

d) Hypothalamus

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39
Q

Wk9D1: Which part of the body does the following:

  • removes heat through sweating
  • generates heat?
A

Skin

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40
Q

Wk9D1: Which part of the body does the following:

*generate heat through shivering and biochemical reactions?

A

Muscles

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41
Q

Wk9D1: Eicosanoids are synthesized from what molecules in the cell?

a) Glucose
b) Fatty acids
c) Nucleic acids
d) Carbohydrates
e) Proteins

A

b) Fatty acids

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42
Q

Wk9D1: What else is used in the production/synthesis of Eicosanoids besides a fatty acid?

A

amino acids

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43
Q

Wk9D1: A fever in the human body is mainly due to what?

a) Resetting of the body’s thermostat
b) Generation of heat by the body
c) Cooling of the body
d) Rapid breathing
e) All of the above

A

a) Resetting of the body’s temperature

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44
Q

Wk9D1: The body is cooler in the morning and throughout the day the body gets warmer.

True/False

A

True

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45
Q

Wk7D2: How are amino acids needed differently in the body?

A
  • Production of proteins and enzymes
  • synthesis and production of ATP
  • Alanine plays a part in the glucose-alanine cycle by transferring nitrogen from tissues back to the liver.
  • Glycine plays a role in halting neurotransmitters that process motor and sensory information which affects:
  • Movement
  • Vision
  • audition
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46
Q

Wk7D2: How can amino acids produce glucose?

A

It’s produced using alanine and glucose-alanine cycle.

  • alanine is formed from pyruvate (circulates nitrogen from muscle to liver)
  • liver collects plasma alanine and reverse transamination and increases urea production
  • pyruvate found in alanine is oxidized or converted to glucose thru gluconeogenesis
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47
Q

Wk7D2: What is used in the redox reactions in the conversion of amino acids?

A

NADH (reduced form) and NAD+ (oxidized form)
FADH and FAD+

Energy is being used.

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48
Q

WK7D2: What is transamination used for?

A

It is important in the formation of nonessential amino acids thru enzymes known as aminotransferases

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49
Q

WK7D2: What other important biological molecules can be made from amino acids?

A

fatty acids (lipids)

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50
Q

WK8D2: Where is the major site of nucleotide metabolism?

A

metabolic requirements are based on dietary intake or they are synthesized from scratch (purines and pyrimidines)

Purines occurs in the liver

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51
Q

WK8D2: Where are purines synthesized?

A

Liver

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52
Q

WK9D1: Eicosanoids are derived from what?

A

Arachidonic acids

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53
Q

WK9D1: How are Leukotrienes and lipoxins synthesized and from what source?

A

Synthesized from arachidonic acids via the linear pathway (enzyme 5-lipoxygenase)

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54
Q

WK9D1: How are Prostaglandins and thromboxanes synthesized and from what source?

A

Synthesized from arachidonic acid via the cyclic pathway (enzyme PGS-cyclooxygenase)

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55
Q

WK9D1: How is the cyclic pathway initiated?

A

initiated thru the action of prostaglandins G/H synthase (prostaglandin endoperoxide synthase-PGS)

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56
Q

WK9D1: What two cyclooxygenases are both catalyze the 2-step conversion of arachidonic acid to PGG2 and then to PGH2?

A

COX-1 and COX-2

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57
Q

WK9D1: Which COX is inducible and expressed in macrophages and monocytes in response to inflammation?

A

COX-2

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58
Q

WK9D1: Which COX is expressed in gastric mucosa, kidney, platelets, and vascular endothelial cells?

A

COX-1

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59
Q

WK9D1: During the cyclic pathway the enzyme PGS possess two activities, what are they?

A

Cyclooxygenase and Peroxidase

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60
Q

WK9D1: How is the linear pathway initiated?

A

Initiated thru the action of LOX’s (lipoxygenase)

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61
Q

WK9D1: How many parts can LOX (lipoxygenase) be divided into? What are they?

A

3 forms; 5-LOX, 12-LOX, and 15-LOX

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62
Q

WK9D1: Which LOX produces leukotrienes?

A

5-LOX

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63
Q

WK9D1: How do the inflammatory mediator elicit response?

A

Eicosanoids produce a wide range of biological effects on inflammatory responses (predominately those of the joints, skin, and eyes) on the intensity and duration of pain and fever, and on reproductive function (including labor)

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64
Q

WK9D1: What other important roles do inflammatory mediators play a part in?

A

Inhibiting gastric acid secretion

Regulating blood pressure through vasodilation or vasoconstriction

inhibiting or activating platelet aggregation and thrombosis

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65
Q

WK9D1: What is a fever and what causes it?

A

Fever occurs when there is an elevated body temperature that is higher than normal daily variations.

It occurs due to an increase in the hypothalamic set point which is usually between 37-39*C

(high body temp caused by the immune system when it attempts to fight an infection)

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66
Q

WK9D1: What are the 2 types of signals that tightly maintains temperature?

A

Peripheral nerves and temperature of the blood in the region

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67
Q

WK9D1: How tightly is the body temperature maintained?

A

Tightly maintained through a process that allows the body to maintain its core internal temperature called thermoregulation

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68
Q

WK9D1: What area of the body is responsible for thermoregulation?

A

Hypothalamus

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69
Q

Wk9D1: How does the body regulate the temp?

A

Body temp is regulated by the “set point of the hypothalamus”

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70
Q

WK9D1: How does the body lower its temperature? Give an examples

A

By vasodilation which leads to heat loss and sweating

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71
Q

WK9D1: How does the body raise its temperature?

A

By vasoconstriction which is first noticed in the hands and feet, causing a reduction in heat loss from the skin

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72
Q

WK9D1: What is an example of how the body raises its temp?

A

Shivering can induce body temperature to rise due to heat production in the muscles

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73
Q

WK9D1: What is Hyperthermia?

A

Uncontrolled increase in body temperature that exceeds the body’s ability to lose heat

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74
Q

WK9D1: What is Hypothermia?

A

Occurs when the body loses heat and can’t produce heat fast enough to compensate for the loss

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75
Q

WK9D1: What is the widely used class of drugs used to treat a fever?

A

NSAIDs

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76
Q

WK9D1: NSAIDs, indomethacin and phenylbutazone all act upon the cyclooxygenase activity by doing what?

A

Inihibiting both COX-1 and COX-2

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77
Q

WK9D1: What is arachidonic acid? Where is it found?

A

Polyunsaturated omega-6 fatty acid

Found in the liver, brain and glandular organs

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78
Q

WK9D1: What is phospholipase A2 and what role does it play in the production of arachidonic acid?

A

Phospholipase A2 (PLA2) is the key enzyme to initiate arachidonic cascade and eicosanoid production

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79
Q

WK9D1: A (20:4 cis D5, 8, 11, 14) is converted to what started by COX enzymes?

A

arachidonic acid is converted to prostaglandins and thromboxanes by COX enzymes

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80
Q

WK9D1: What is the difference between COX-1 and COX-2?

A

COX-1 and COX-2 are expressed differently
COX-1 : runs all the time
COX-2 : has to be turned on

different gene products but both isoenzyme families

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81
Q

WK9D1: Why do drug companies target COXs with NSAIDs?

A

NSAIDs could inhibit the COX-1 and COX-2 and other drugs can’t

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82
Q

WK9D1: A (20:4 cis D5, 8, 11, 14) is converted to what started by LOX enzymes?

A

arachidonic acid is converted to leukotrienes by the LOX enzymes known as lipoxygenase

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83
Q

WK9D1: Are these inflammatory mediators short or long acting? Why?

A

Short acting and quickly degraded in the tissue (this is why you have to take NSAIDs more often)

If they were long acting, the drugs would not act the same because they would degrade slower.

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84
Q

WK9D1: What are some ways to bring down a fever?

A

NSAIDs, placing a damp towel on forehead, drinking fluids, lukewarm bath

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85
Q

WK9D1: What is defined a fever by clinicians?

A

100.4*F

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86
Q

WK9D1: When is a high body temperature not a fever? Be specific

A

Hyperthermia, which can lead to heat stroke (not regulated, body can no longer fight the increase in temp)

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87
Q

WK9D2: Where does the extrinsic and intrinsic pathways intersect?

A

Coagulation cascade

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88
Q

WK9D2: Name the 3 types of mechanisms that maintains hemostasis.

A
  1. Vasoconstriction (vascular spasm)
  2. Formation of platelet plug
  3. Coagulation (blood clot)
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89
Q

WK9D2: Which pathways are involved when a blood clot is formed?

A

Intrinsic and extrinsic

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90
Q

WK9D2: What are the intrinsic and extrinsic pathways?

A

Intrinsic: activated by negatively changed surfaces in vitro (fibrins proteins stick together to form a clot)

Extrinsic: fibrin clot formation due to tissue damage (ex: external trauma or a sharp object breaking the barrier of the skin and causing blood to bleed)

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91
Q

WK9D1: Which NSAIDs are preferred for children?

A

Motrin or Tylenol

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92
Q

WK9D1: What are key regulatory points in the biosynthesis?

A

Eicosanoids are key mediators and regulators of inflammation and immunity

COX and LOX are inhibited because it’s the rate-limiting step

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93
Q

WK9D1: How do the inflammatory mediators elicit the response?

A

Response is elicited by phagocytes releasing by cytokines and lipid messengers

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94
Q

WK9D2: In general, which type of enzymatic reactions are involved in the activation of the various humoral clotting factors in the clotting cascade?

A) kinase 
B) Protease
C) Nuclease
D) Caspase
E) Phosphatase
A

B) Protease

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95
Q

WK9D2: What is the term that is used when the enzymes are inactive?

A

Zymogens

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96
Q

Wk9D2: All the humoral protein factors involved in the clotting cascade are secreted in the enzymatically active form.

True/False

A

False

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97
Q

Wk9D2: Platelets can only be activated by binding to collagen.

True/False

A

False

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98
Q

WK9D2: What are some other ways platelets can be activated?

A

Thrombin, ADP and Prostacyclin

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99
Q

WK9D2: The clotting cascade is a series of phosphorylation events to activate the proteins.

True/False

A

False

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100
Q

Wk9D2: Why do the numbers of the factors not go in order of their activation?

A

They are names in the order in which they were discovered

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101
Q

Wk9D2: What role do the endothelial cells play in the clotting cascade? Why is this important when it comes to vascular disease?

A
  • increases calcium
  • produce anticoagulants
  • line the vessels inside and under the basement membrane
  • acts as a barrier against activation
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102
Q

WK9D2: How does Coumadin inhibit clotting?

A

Inhibits vitamin K

long acting ~12-14 hours

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103
Q

Wk9D2: What role in clotting do platelets play? Do they signal? If so how?

A
  • role in aggregation
  • signal from outside to inside
  • Platelets bind to collagen at the site of the vessel wall injury, form thromboxane A2 and release ADP to activate other platelets flowing by the vicinity of injury
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104
Q

WK9D2: How does Heparin inhibit clotting?

A

Heparin inhibit thrombosis by inactivation activated Factor X and inhibiting the conversion of prothrombin to thrombin

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105
Q

WK9D2: In the blood clotting cascade, what protein factor is the target point where both the extrinsic or intrinsic activation pathways come together?

A) Xa to X
B) X to Xa
C) Va to V
D) Fibrinogen to Fibrin
E) Prothrombin to Thrombin
A

B) X to Xa

“a” means it’s activated

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106
Q

Wk9D2: Why is having a cascade more important than a single event?

A

Highly regulated, allows for localization/ very focal, allow for on-demand availability

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107
Q

WK9D2: What is the difference between hemostasis and thrombosis?

A

Hemostasis normal response of the vessel to injury by forming a clot that serves to limit hemorrhage (has an extra step: vasoconstriction)

Thrombosis is pathological clot formation that results when hemostasis is excessively activated in the absence of bleeding

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108
Q

WK9D2: How is hemostasis initiated?

A

Hemostasis is initiated by blood vessel damage/cuts

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109
Q

WK9D2: How is thrombosis initiated?

A

Initiated by damaged to the endothelial lining of the blood vessel

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110
Q

WK9D2: What does hemostasis and thrombosis have in common?

A

Both lack nucleic acids, converge to form FACTOR Xa, same last 3 steps to stop blood loss

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111
Q

WK9D2: What type of enzymatic functions do the clotting factors possess?

A

Enzymatic cleavage

112
Q

WK9D2: How is the enzymatic activity controlled? What is the termed used for these enzymes that are produce inactive and then activated enzymatically?

A

Zymogens are coagulation factors that are initially inactive but become activated when they are clipped by a serine protease

113
Q

WK9D2: What must happen to fibrin to strengthen and stabilize the fibrin mesh?

A

Fibrin binds to platelets and stabilized the hemostatic plug

114
Q

WK9D2: Which factor is involved when fibrin is used to be a stabilizer and strengthener?

A

Factor 13; cross links fibrin to stabilize clot

115
Q

WK9D2: How does the clot break down and what is released?

A

Enzyme of plasmin is responsible for these conversions

  • prothrombin to thrombin
  • fibrin to fibrinogen
  • plasminogen to plasmin
116
Q

WK9D2: What are the 3 steps that hemostasis and thrombosis share?

A

1) platelet bind to collagen, platelet plug formation
2) Formation of fibrin mesh, clot formation/coagulation
3) plasmin dissolves the clot

117
Q

WK9D2: What is the coagulation pathway and what are the factors involved?

A

Coagulation pathway forms thrombin, it’s the process by which blood forms clots.

May coagulation factors are zymogens pf serine proteases

118
Q

WK9D2: How are the intrinsic and extrinsic pathways regulated?

A

it goes from inactive to activated by zymogens that cleave enzymes giving it a short half life

119
Q

WK9D2: What are the consequences when one of the factors is missing?

Example

A

Impaired ability for blood to coagulate which can lead to excessive bleeding.

Hemophilia A & B

120
Q

WK9D2: What type of enzymes are involved in the cascade? How is this important?

A

Zymogens of serine protease

Coagulation factors that become activated then inactivated during the overall process

121
Q

WK9D2: What are t-PA and streptokinase and what are they used for?

A

Tissue plasminogen activator is a serine protease that is released into the circulation from vascular endothelium under conditions of injury or stress and is catalytically inactive unless bound to fibrin.

122
Q

WK9D2: What role does collagen play in platelet aggregation?

A

Platelets bind to collagen at the site of vessel wall injury, form thromboxane A2 and release all of it’s granules (ADP) which activate other platelets flowing by the vicinity of the injury.

123
Q

WK10D1: Adult hemoglobin is in either a T-form (oxygen low affinity) or R-form (oxygen high affinity) state caused by a change in shape of the proteins?

True/False

124
Q

WK10D1: Which role below does not fit with hemoglobin’s function in the body?
A) Carry H+
B) Carry O2
C) Buffer the blood pH
D) Specifically bring iron (Fe2+) in a coordinated location
E) none of the above

A

E) none of the above

125
Q 
WK10D1: For hemoglobin to function properly in binding oxygen, it requires the iron to be in what state?
A) Fe2+
B) Fe1+
C) Fe3+
D) Fe0
E) Fe2-
F) Fe3-
126
Q

WK10D1: Myoglobin binds O2 with the same affinity and carries it to the muscle in the RBC like hemoglobin.

True/False

A

False

  • Myoglobin has a higher affinity
  • in the muscles
  • hyperbolic function
127
Q

WK10D1: Which statement below is correct for the function of fetal hemoglobin?

A)The fetal curve is shifted to the right of the adult hemoglobin indicating a higher affinity for O2.

B) The fetal curve is shifted to the left of the adult hemoglobin indicating higher affinity for O2.

C) The fetal curve is identical to that of adult hemoglobin.
The fetal curve is shifted to the left indicating a lower affinity for O2.

D) The fetal curve is shifted to the left indicating a lower affinity for H+

A

B) the left of the adult hemoglobin indicating higher affinity for O2.

128
Q

WK10D1: Under what conditions (physiologically) would you not saturate the hemoglobin in the lungs?

A

In high altitude

129
Q

WK10D1: How is CO2 carried back to the lungs from the tissues where it is produced? What enzymes is involved?

A

CO2 binds to hemoglobin, some turns into hydrogen bicarbonate.

enzyme: carbonic anhydrase

130
Q

WK10D1: How does hemoglobin act as a buffer?

A

Stabilized T state; take up H+ proton in kreb cycle and respiratory system

131
Q

WK10D1: How does this mutation cause the “sickling” shape of the RBC under what condition?

A
  • Inherited abnormal hemoglobin -> distorted (sickle) shape of RBC
  • mutation in the hemoglobin-beta gene –> causing the hydrophilic amino acid glutamic acid to be replaced with the hydrophobic amino acid
132
Q

WK10D1: What are the physiological consequences of the sickle shape?

A

Hypoxia –> brain

sickle cells can get stuck and block blood flow –> pain and infection

133
Q

WK10D2: How are chromosome abnormalities analyzed and what methods are used?

A

!) Standard cytogenetic analysis

2) Molecular cytogenetics
3) Array-based methodologies (cytogenomics)
4) Next-Generation Sequencing- Based methodologies

134
Q

WK10D2: How do the methods work to analyze the abnormalities?

A

Probes, fluorescence and scanning

135
Q

WK10D2: What types of chromosome abnormalities take place?

A

1) Numerical chromosome abnormalities

2) structural chromosome abnormalities

136
Q

WK10D2: What are the 5 different structural abnormalities?

A

1) Deletions
2) Duplications
3) Translocation
4) Inversions
5) Uniparental Disomy

137
Q

WK10D2 (Structural chromosome abnormalities): Loss of chromosomal segment

138
Q

WK10D2 (Structural chromosome abnormalities): inheritance of a pair of chromosomes from only one parent

A

Uniparental disomy

139
Q

WK10D2 (Structural chromosome abnormalities): exchange of chromosomal segments between at least 2 chromosomes

A

translocations

140
Q

WK10D2 (Structural chromosome abnormalities): rearranged segment, where there are two breaks within a chromosome, with the intervening chromosomal material inserted in an inverted orientation

A

inversions

141
Q

WK10D2: How do the chromosome abnormalities take place?

A

Cell replication occurs in mitosis and meiosis (meiosis is an inherited trait) which is where chromosome abnormalities can occur (in metaphase)

142
Q

WK10D2: How can chromosome abnormalities cause cancer?

A

Fusing protein: turning 2 proteins on together that shouldn’t be together

143
Q

WK10D2: Errors in mitosis are what leads to an extra chromosome being passed onto the child.

True/False

A

False

Correct answer: Meiosis

144
Q

WK10D2: An individual can not survive if they have an extra chromosome.

True/False

A

False

Example: Down Syndrome - Chromosome 21

145
Q

WK10D2: Which method below would not be used to analyze chromosome abnormalities?

A) FISH
B) G-banding
C) ARRAY
D) Protein sequencing
E) None of the above
A

D) Protein sequencing

DNA being sequencing and gets mutated not proteins

146
Q

WK10D2: Maternal age is a factor in developing chromosome abnormalities.

True/False

A

True

Eggs in the women just sits in the G0 phase and accumulate mutations as they just wait to be dropped so abnormalities will form when the female final gets pregnant.

147
Q

WK10D2: Aneuploidy is best described as the loss or gain of a chromosome.

True/False

148
Q

WK10D2: This is a type of numerical chromosome abnormality that takes place when there are 2 or more population of cells with distinct chromosome constitution.

149
Q

WK10D2: This is a type of numerical chromosome abnormality that takes place when there are an extra or missing chromosome.

A

Aneuploidy

150
Q

WK10D2: An example of aneuploidy is:

A

Down Syndrome

151
Q

WK10D2: An example of mosaicism is:

A

Turner Syndrome

152
Q

WK10D2: (Type of method used to analyze chromosome abnormalities): allowed for the staining of chromosomes so that each chromosome could be recognized by its pattern of alternating dark and light

A

Chromosome Banding

153
Q

WK10D2: (Type of method used to analyze chromosome abnormalities): Exam of banded chromosomes which allow for the determination of the number and identity of chromosomes in a cell

A

Standard Cytogenetic analysis

154
Q

WK10D2: (Type of method used to analyze chromosome abnormalities): links chromosome and molecular analysis as well as overcome some limitations of standard cytogenetics

A

molecular cytogenetics

155
Q

WK10D2: FISH is an example of which type of method used to analyze chromosome abnormalities?

A

Molecular Cytogenetics

156
Q

WK10D2: This is a type of molecular cytogenetic method which allows the determination of the number and location of specific DNA sequences; identify structural alterations thru probes that map both sides of translocation breaking point.

A

FISH Fluorescence in situ Hybridization

157
Q

WK10D2: (Type of method used to analyze chromosome abnormalities): DNA based instead of cell based and allows for scanning of genomes for small deletions and duplications

A

Array-based methodologies

158
Q

WK10D2: (Type of method used to analyze chromosome abnormalities): detects clinically relevant intragenic mutations and well soon allow the complete analysis of a patient’s genome

A

next generation sequencing

159
Q

WK10D2: (Type of possible effects of chromosome abnormalities): this is a type of aneuploidy with a low birth weight, ocular malformation, cleft lip and palate, postaxial polydactyly, cardiac defects and renal malformation

A

Trisomy 13

160
Q

WK10D2: (Type of possible effects of chromosome abnormalities): this is a type of aneuploidy when neonates have distinct characteristics with an abnormal neurologic exam, underdeveloped genitalia, lack of responsiveness, congenital heart disease, esophageal atresia, omphalocele

A

Trisomy 18

161
Q

WK10D2: How can chromosome abnormalities cause cancer?

A

When a chromosome change confers, a growth or proliferation advantage on the cell is a consequence of mosaicism that occurs in meiosis or mitosis of a cell

162
Q

WK10D2: When would the chromosome abnormality be fix in the genetics and passed on?

A

Meiosis: sex cell replication

from diploid to haploid

allows for chromosome recombination

163
Q

WK10D2: How do you analyze the changes in chromosome aberrations?

Small to large or large to small

A

Large to small

164
Q

WK11D1: How is DNA packages in the eukaryotic cell?

A

Chromatins made up of condensed DNA (histones)

165
Q

WK11D1: What levels of packing are achieved?

A
  • Naked Double-helical DNA
  • Fibril of nucleosomes
  • chromatin fiber of super helical nucleosomes
  • condensed metaphase chromosome loops
166
Q

WK11D1: What proteins allow this packing to happen?

A

Nucleosomes

H2A and H2B

H3 and H4

167
Q

WK11D1: Which types of histones form dimers?

A

H2A and H2B

168
Q

WK11D1: Which types of histones form tetramers?

169
Q

WK11D1: What are nucleosomes?

A

composed of DNA wound around an octameric complex of histone molecules

170
Q

WK11D1: What are the 4 major types of histones?

A

H2A
H2B
H3
H4

171
Q

WK11D1: How is a chromosome described structurally?

A

Two-fold symmetry

172
Q

WK11D1: What are the parts of a chromosome?

A

2-fold symmetry with identical sister chromatids connected by a centromere and the end of each chromosome contains a telomere

*made up of condensed and noncondensed loops

173
Q

WK11D1: What does the noncondensed loops consist of?

A

Chromatin fibrils composed of nucleosomes

174
Q

WK11D1: How are genes arranged on chromosomes?

A

1) Active
2) Inactive
3) Constitutive
4) Facultative

175
Q

WK11D1: (Arrangement on chromosomes definitions): densely packed during interphase; heterochromatin

176
Q

WK11D1: (Arrangement on chromosomes definitions):always condensed and found near the centromere and telomeres

A

constitutive

177
Q

WK11D1: (Arrangement on chromosomes definitions): at times is condensed while other times is inactive (transcribing)

A

facultative

178
Q

WK11D1: (Arrangement on chromosomes definitions): large region that are more sensitive to digestion by nuclease; euchromatin

179
Q

WK11D1: This mechanism allows for the rearrangement of chromosomal DNA by removal or insertion of one or more bases that results in an altered gene product or the alteration of gene expression when non-protein coding DNA is involved

180
Q

WK11D1: This mechanism allows for the rearrangement of chromosomal DNA by exchange of genetic information between similar chromosomes that occurs mostly in meiosis and requires that homologous metaphase chromosomes be coordinated

A

Recombination

181
Q

Wk11D1: What is a jumping DNA and how is it important to gene expression?

A

Small DNA elements that aren’t viruses and are capable of transposing themselves in and out of a host genome in ways that affect surrounding genomes

182
Q

Wk11D1: How does DNA replication initiate and where?

A

only occurs with single-stranded DNA template

interaction with proteins at the ORI initiates replication due to protein-protein and protein-DNA interactions

Origin of replication

183
Q

Wk11D1: What protein classes are involved in DNA replication?

A 
DNA polymerase
Topoisomerase
Helicase
DNA Primase
Single-stranded binding protein
DNA Ligases
184
Q

Wk11D1: Which protein class initiates synthesis of RNA primers?

A

DNA Primase

185
Q

Wk11D1: Which protein class seals single strand nick between nascent chain and Okazaki fragments on lagging strand?

A

DNA Ligase

186
Q

Wk11D1: Which protein is ATP-driven by unwinding of DNA?

187
Q

Wk11D1: Which protein class relieves torsional strain that is caused by helicase unwinding?

A

Topioisomerase

188
Q

Wk11D1: Which protein prevents premature hardening of ssDNA that leads to dsDNA?

A

Singe-stranded Binding Protein

189
Q

Wk11D1: Which protein is deoxynucleotide polymerization?

A

DNA polymerase

190
Q

Wk11D1: What steps must take place for DNA to replicate?

A

1) identification of ORI
2) ATP hydrolysis0driven removal of nucleosomes and unwinding of dsDNA to provide single-strand template
3 )formation of replication fork and synthesis of RNA primer
4) Initiation of DNA synthesis and elongation
5) Formation of replication bubble
6) Reconstitution of chromatin structure

191
Q

Wk11D1: What is a replication bubble?

A

an unwound and open region of a DNA helix when DNA replication occurs

192
Q

Wk11D1: What are leading and lagging strands?

A

Leading: DNA synthesis occurs continuously

Lagging: DNA synthesis occurs discontinuously in fragments

193
Q

Wk11D1: What are the DNA fragments called and where do they occur?

A

Okazaki fragments on the lagging strand

194
Q

Wk11D1: Why does leading and lagging strands occur?

A

The formation of leading and lagging strands allows for primase to be formed, allowing polymerase to begin synthesizing

195
Q

Wk11D1: What types of damages can occur to DNA?

A

1) Single-base Alteration
2) Two-base Alteration
3) Chain Breaks
4) Cross-linkage

196
Q

Wk11D1: What causes the damage in single-base alteration?

A

depurination: release of adenine or guanine

Deamination of cytosine to uracil

deamination of adenine to hypoxanthine

Alkylation of base

base analog incorporation

197
Q

Wk11D1: What causes the damage in a two-base alteration?

A

1) UV light-induced thymine-thymine (pyrimidine) dimer

2) Bifunctional alkylating agent cross-linkage

198
Q

Wk11D1: Ionizing radiation, radioactive disintegration of backbone element and oxidative free-radical formation cause which type of DNA damage?

A

Chain breaks

199
Q

Wk11D1: what causes the damage in a cross-linkage?

A

1) between bases in same or opposite strands

2) between DNA and protein molecules (histones)

200
Q

Wk11D1: What are ways that the different lesions can be repaired?

A

1) Mismatched repair
2) base excision repair
3) nucleotide excision repar
4) homologous recombination
5) nonhomologous end-joining

201
Q

Wk11D1: The only enzyme involved in DNA replication is the DNA polymerase.

True/False

A

False

RNA transcriptase/DNA polymerase

DNA ligase
Helicase
Topoisomerase

202
Q

Wk11D1: DNA is always enzymatically synthesized in the 5’ to 3’ direction.

True/False

203
Q

Wk11D1: During DNA replication, the leading strand is made in fragments and the lagging strand is made continuously.

True/False

A

False

Leading: continuously
Lagging: fragments

204
Q

Wk11D1: The only errors that can happen to the DNA sequence are caused by ionizing radiation.

True/False

A

False

long wave radiation
Base excision repair
bulking lesion

205
Q

Wk11D1: Why is bulking lesions easier to recognize?

A

It’s a dimer

206
Q

Wk11D1: The double stranded DNA in a Eukaryotic cell is coiled around histones and looped into higher order structures to form chromosomes.

True/False

207
Q

Wk11D1: What are the levels of DNA packaging?

A

1) Naked DNA
2) Beads-on-a-string
3) nucleosomes
4) non-condensed loops
5) condensed loops
6) metaphase chromosome

208
Q

Wk11D1: Describe how nucleosomes and packing of the DNA can be used to regulate gene expression.

A

Inactive and active form

inactive- more densely packed

209
Q

Wk11D1: Why is the origin of replication an AT rich sequence?

A

AT is less stable than a GC bond

210
Q

Wk11D1: What problem must be overcome in the replication bubble?

A

conversion of RNA

211
Q

Wk11D1: Both the leading and lagging strand synthesize in the 5’ to 3’ direction.

True/False

212
Q

Wk11D1: DNA replication is initiated at specific sites to generate a replication bubble and it only occurs during the S phase of the cell cycle.

True/False

213
Q

Wk11D1: DNA polymerase can add nucleotide only to the 3’ end of the DNA strand.

True/False

214
Q

Wk11D2: What is a promoter?

A

A distinct site on the DNA templates that enzymes attach to before the beginning of RNA synthesis.

215
Q

Wk11D2: What is region where RNAP binds to DNA with a higher affinity?

A

Promoter region

216
Q

Wk11D2: What are the transcription cycle steps?

A

1) template binding and closed RNA polymerase-promoter complex formation
2) open promoter complex formation
3) chain initiation
4) promoter clearance
5) chain elongation
6) chain termination and RNAP release

217
Q

Wk11D2: What transcribes the DNA into RNA?

A

RNA polymerase enzyme

218
Q

Wk11D2: What are the classes of transcription factors involved in mRNA gene transcription?

A

1) Basal components
2) Coregulators
3) Activators

219
Q

Wk11D2: What is termination and how does it happen?

A

Occurs when transcription comes to an end and RNA polymerase crosses a stop (termination) sequence in the gene

220
Q

Wk11D2: What are the stop codons?

221
Q

Wk11D2: What are the 2 mechanisms of termination?

A

1) Bacterial RNAP: can directly terminate transcription

2) Rho-factor-RNAP Interactions: lead to termination

222
Q

Wk11D2: How is RNA processed?

A

it recruits a transcription export to elongation, splices it, and export it

alternative splicing provides an opportunity for increased genetic potential

in nucleus, highly coordinated

223
Q

Wk11D2: What is alternative splicing and what benefit is this to the cell?

A

Form of coupling transcription and mRNA processing

provides for the production of different mRNA from a single mRNA primary transcript

provides tissue-specific regulation of gene expression

224
Q

Wk11D2: What other RNAs are in the cell besides mRNA?

A

rRNA -ribosomal

tRNA- transfer RNA

225
Q

Wk11D2: When DNA is being transcribed from left to right by RNA polymerase to make mRNA, the bottom strand is the template strand or the strand providing the information.

True/False

A

True

I changed the original iRAT question.

(left to right –> bottom is template)

226
Q

Wk11D2: All RNA in the cell is composed of mRNA.

True/False

A

False

rRNA
tRNA

227
Q

Wk11D2: The process by which different mRNAs can be produced from the same gene is?

A) Alternative splicing
B) Translation
C) Transcription
D) Replication
E) Intron
A

A) Alternative splicing

(cutting up the same strand)

example: think about a train, mixing and matching different types of cargos and wagons

228
Q

WK11D2: Which statement below is incorrect? (Circle all that applies)

A) Transcription like replication proceeds in the 3’ to 5’ direction.

B) Promoters in Eukaryotic genes are regulatory sequences.

C) The transcription is performed by Polymerase II
Splicing of mRNA takes place in the cytoplasm

D) Transcription is a tightly regulate process

A

A) Transcription like replication proceeds in the 3’ to 5’ direction.

C) Splicing of mRNA takes place in the cytoplasm

229
Q

WK11D2: What signaling pathways could activate or repress a gene? HOW?

A

GPCR signaling transduction pathway

  • Calcitonin increase
  • Vasopressin increase
  • Dox decrease
  • allosteric change during phosphorylation
230
Q

WK11D2: What are the steps in the production of mRNA?

A

1) RNA polymerase produces a “primary transcript” an exact RNA copy of the gene
2) A cap is put on the 5’ end
3) RNA is terminated and poly-A is added to the 3’ end
4) all introns are spliced out
5) at this point, RNA can be called messenger RNA. It is then transported out of the nucleus into the cytoplasm, where it is translated

231
Q

WK11D2: What is the potential consequence if an intron is not spliced out?

A

Intron retention

When not removed, it will remain as part of the final RNA molecule

  • frameshift with premature stop codons (truncated proteins)
  • incorrect skipping of exons

Beta-thalassemia

232
Q

Define Aggregation

A

Formation of a number of things into a cluster

aka “cluster formation”

233
Q

Review: What would be the best and most energy efficient way to interconvert the nucleotides?

A

Make triphosphates from monophosphates

234
Q

WK9D2: What are the 3 types of clots (thrombin) formed?

A

1) White thrombus
2) Red Thrombus
3) Fibrin deposits

235
Q

WK9D2: What is a clot composed of and how does it form? How is a clot dissolved?

A

Clots are composed of fibrinogen which is converted to fibrin by thrombin.

degraded by serine protease known as plasmin

236
Q

WK9D2: Coagulation Factors include

A 
VIII (8)
IX (9)
X (10) * V (5)
XI (11)
XII (12) 
prothrombin
237
Q

WK9D2: Factor VIII deficiency results in

A

hemophilia A (X-linked)

238
Q

WK9D2: Factor IX deficiency results in

A

hemophilia B (X-linked)

239
Q

WK9D2: Factor XI deficiency results in

A

hemophilia C

240
Q

WK9D2: What is the most common hereditary bleeding disorder?

A

von Willebrand disease results in a deficiency of von Willebrand Factor

241
Q

WK9D2: Which type of enzyme leads to conversion of fibrinogen to fibrin monomers in the cascade?

242
Q

WK9D2: Which lab test is used to measure the extrinsic pathway of coagulation, thrombosis and platelet aggregation?

A

Prothrombin time

also measures effectiveness of warfarin

243
Q

WK9D2: Which lab test is used to measure the intrinsic pathway of coagulation, thrombosis, and platelet aggregation?

A

Activated partial thromboplastin time

also monitors heparin therapy

244
Q

WK1D1: ALL transport of molecules into or out of the cell require energy in the form of ATP.

True/False

245
Q

WK1D1: The cytoskeleton in the Eukaryotic cell is composed of the same carbohydrate molecules as the found in a bacteria cell wall since both provide structure to the cell.

True/False

246
Q

WK1D1: What building blocks are common to both Prokaryotic and Eukaryotic cell? (Circle all that applies)

A) DNA
B) Carbohydrates
C) Lipids
D) Amino Acids

A

A) DNA
B) Carbohydrates
C) Lipids
D) Amino acids

247
Q

WK1D1: Like bacteria, Human Eukaryotic cells have membranes and cell walls to provide for structural integrity and rigidity.

True/False

248
Q

WK1D2: The typical mammalian cell contains only a type of transporter like aquaporin to move all molecules across the membrane into the cell.

True/False

A

False

Another transporter: sodium-potassium pump. ABC family transporter

249
Q

WK1D2: A membrane channel or pore can ONLY more molecules in one-direction.

True/False

A

False

pore is a hole in a cell membrane made a specific protein to allow certain substances and dictate what could pass

250
Q

WK1D2: Characteristics which affect the diffusion of a molecule across the membrane are?

A) Hydrophobicity
B) Charge
C) Size
D) All of the above

A

D) All of the above

251
Q

WK1D2: Proteins which are associated and not integrated with the outer membrane are primarily interacting with the hydrophobic tails of the membrane.

True/False

A

False

The hydrophobic tails are on the inside.

252
Q

WK1D2: The outer membrane of a cell forms with the polar head groups of the lipids on the outside with the hydrophobic tails inside way from the water.

True/False

253
Q

WK2D2: Components of the extracellular matrix contains proteins and can also contain carbohydrate.

True/False

254
Q

WK2D2: Collagen Type 2 is the only component of the extracellular matrix.

True/False

A

False

Collagen I - bone
Collagen II - cartilage

255
Q

WK2D2: ALL receptors involved in signaling are integrated into the plasma membrane.

True/False

A

False

some are peripheral; steroid receptors go to the nucleus

256
Q

WK2D2: Which amino acid(s) listed below would be a substrate for a kinase to phosphorylated it? (Circle all that applies)

A) Tyrosine
B) Serine
C) Threonine
D) Cysteine
E) Histidine
A

A) Tyrosine
B) Serine
C) Threonine

257
Q

WK2D2: Which item listed below is NOT involved in some way in signal transduction for the cell?

A) Protein kinase
B) Small cyclic nucleotide
C) Membrane receptor protein
D) Phosphorylated proteins
E) None of the above
A

E) None of the above

258
Q

WK3D1: More than one signaling pathway can be integrated to lead to a cellular response.

True/False

259
Q

WK3D1: Which item below would be a common theme amongst the signaling pathways?

A) PO4
B) SO4
C) AMP
D) ATP
E) ADP
A

A) PO4

GDP (inactive)
–hydrolyze –>
GTP (active)

GDP + PO4 = GTP

260
Q

WK3D1: GPCR are made up of multiple subunits besides the seven membrane spanning regions.

True/False

A

True

Tyrosine kinase dimerization

261
Q

WK3D1: When the ligand binds to its specific G-protein coupled receptor, it always leads to up-regulation as the final end product.

True/False

A

False

Negative response (down regulation)

Positive response
(up regulation)

262
Q

WK3D2: The reason chemotherapy works so well on cancer cells is because they are in the G0 phase of cell cycle.

True/False

A

False

G0 - rapidly growing cells

Most radiosensitive - G1 & M phase

263
Q

WK3D2: Which item below is NOT associated with the cell cycle?

A) CDK
B) Cyclins
C) Checkpoints
D) Phosphorylation
E) GDP
264
Q

WK3D2: Most cells in the body typically “hang out” in G0 phase of the cell cycle.

True/False

265
Q

WK3D2: The order of the phases of the cell cycle are:

A) G1 > S > M > G2
B) S > G1 > G2 > M
C) M > S > G1 > G2
D) G1 > S > G2 > M
E) G1 > M > G2 > S
F) Random order
A

E) G1 > M > G2 > S

G1- cell growth
S- genome replication
G2- produces histones to nuclear proteins, prep for cellular division
M- cell division

266
Q

WK3D2: The cell cycle is a disorganized random series of evens when a cell undergoes cellular division.

True/False

267
Q

WK4D1: Which cellular organelle listed below is centrally involved in either necrosis or apoptosis of the cell?

A) Mitochondria
B) Nucleus
C) ER
D) Golgi
E) All are correct
A

A) Mitochondria

268
Q

WK4D1: During the process of programmed cell death, what family of enzymes are activated with increase Ca2+?

A) Caspase-protease
B) Caspase-nuclease
C) Chaperone-protease
D) Chaperone-nuclease
E) Proteasome
F) Cyt-C
A

A) Caspase-protease

269
Q

WK4D1: Apoptosis and necrosis both result in cell death with the same outcome that the cell is phagocytosed to minimize inflammation.

True/False

270
Q

WK5D1: Which statement below would be correct concerning metabolism?

A) Tightly regulated
B) Not regulated
C) Not energy controlled
D) All of the above
E) None of the above
A

A) Tightly regulated

271
Q

WK5D1: Which item(s) listed below are involved in metabolism?

A) Organs
B) Cells 
C) Blood
D) Mitochondria
E) All of the above
A

E) All of the above

272
Q

WK5D1: Catabolism is the process of breaking down complex molecules to simple molecules and energy production.

True/False

A

True

CO2, Water, NH3

273
Q

WK5D1: The cell can produce energy from only lipids.

True/False

A

False

Carbohydrate - cellulose

Proteins- glucose

274
Q

WK5D1: Metabolism consists of only catabolism.

True/False

A

False

Anabolism - building of small molecules into complex ones

275
Q

WK5D2: Inhibitors of enzymes reactions inhibit by one mechanism only.

True/False

A

False

Competitive and noncompetitive

276
Q

WK5D2: Enzyme reactions only go in one direction (substrate to product).

True/False

277
Q

WK5D2: The [S] in the Michaelis-Menten equation describes what about the substrate?

A) Amount in (liters) -> Km
B) Concentration in (grams)
C) Quantity in (grams)
D) Concentration (moles/liter)
E) Amount in (moles)
A

A) Amount in (liters) -> Km

P1: Ben & Maytee Fisch College of Pharmacy (6 decks)

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