Biochem Final Flashcards
Cumulative (277 cards)
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
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
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)
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)
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
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
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
8
Q
Wk7D2: How are amino acids classified metabolically?
A
nonessential and essential
9
Q
Wk7D2: Name some nonessential amino acids
A
Alanine Asparagine Aspartate Cysteine Glutamine Glycine Proline Serine Tyrosine
10
Q
Wk7D2: Name some essential amino acid
A
Arginine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine
11
Q
Wk7D2: What are the 3 categories that amino acids fall in?
A
Glucogenic
Ketogenic
Glucogenic and Ketogenic
12
Q
Wk7D2: Which group give rise to a net production of pyruvate or TCA cycle intermediates: alpha-ketoglutarate and oxaloacetate?
A
Glucogenic
13
Q
Wk7D2: Which group give rise only to acetyl-CoA or acetoacetyl-CoA?
A
Ketogenic
14
Q
Wk7D2: Lysine and leucine are solely falls under what type of amino acid category?
A
Ketogenic
15
Q
Wk7D2: Which group give rise to both glucose and fatty acid precursors?
A
Glutogenic and ketogenic
16
Q
Wk7D2: Isoleucine, phenylalanine, threonine, tryptophan and tyrosine fall under which category of amino acid?
A
Glutogenic and ketogenic
17
Q
Wk7D2: In aspartate asparagine metabolism what enzyme is important in interconversion?
A
Asparagine synthase: catalyze the conversion of aspartate to asparagine
18
Q
Wk7D2: How can amino acids produce glucose?
A
Gluconeogenesic pathway converts pyruvate, lactate, glycerol and amino acids (alanine and glutamine) into glucose
19
Q
Wk7D2: What is transamination used for?
A
plays a role in synthesis and breakdown of amino acids
20
Q
Wk7D2: What is deamination?
A
removal of an amino group from an amino acid to other compound
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
22
Q
Wk8D2: The development of gout is due to precipitation of uric acid crystals in the joint.
True/False
A
True
23
Q
Wk8D2: Individual nucleotides must be synthesized individually because there is no interconversion possible.
True/False
A
False
24
Q
Wk8D2: In purine biosynthesis of an amino acid is used in the pathway.
True/False
A
True
25
Wk8D2: The de novo synthesis of nucleotides and the salvage pathway are the same pathway.
True/False
False
26
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
b) organ meat or tissue high in cell number
27
Wk8D2: How is nucleic metabolism involved in the disease gout?
uric acid comes from purine metabolism
28
Wk8D2: Uric acid comes from what part of metabolism?
a) Base
b) Sugar
c) Triphosphate
a) Base
29
Wk8D2: What would be some reasons why uric acid would reach such high levels?
* Reduction of uric acid = overproduction
| * not being excreted properly by the kidneys
30
Wk8D2: What are common drugs used to treat gout?
Allopurinol
Colchine
Uloric
NSAIDs (if not bad enough to medicate)
31
Wk8D2: What carbohydrate is used and where does it come into the synthesis pathway?
* Ribose is phosphorylated at the beginning of the pathway
| * AA provide nitrogen for bases
32
Wk8D2: What other building blocks are used in the synthesis?
* AA close the ring of the structure and provide the amino group
* Vitamin: folate and niacin
* ATP
33
Wk9D1: Arachidonic acid is used in the production of leukotrienes.
True/False
True
arachidonic acids is a long chain (20 C) fatty acid; more than one bond; unsaturated; carboxylic group on an end of the chain
34
Wk9D1: What are two ways we can get a substrate as an enzyme?
* Produce it ourselves --> fatty acid
| * Diet
35
Wk9D1: What is the richest fatty acid place in our body?
lipid membrane
36
Wk9D1: The best treatment for a fever would be:
a) Steroids
b) Antibiotics
c) Drinking water
d) Drinking alcohol
e) NSAIDs
e) NSAIDs
| * inhibits COX-1 and COX-2
37
Wk9D1: What is the temperature that is clinically considered as a fever?
100.4*F or 38*C
38
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
d) Hypothalamus
39
Wk9D1: Which part of the body does the following:
* removes heat through sweating
* generates heat?
Skin
40
Wk9D1: Which part of the body does the following:
| *generate heat through shivering and biochemical reactions?
Muscles
41
Wk9D1: Eicosanoids are synthesized from what molecules in the cell?
a) Glucose
b) Fatty acids
c) Nucleic acids
d) Carbohydrates
e) Proteins
b) Fatty acids
42
Wk9D1: What else is used in the production/synthesis of Eicosanoids besides a fatty acid?
amino acids
43
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) Resetting of the body's temperature
44
Wk9D1: The body is cooler in the morning and throughout the day the body gets warmer.
True/False
True
45
Wk7D2: How are amino acids needed differently in the body?
* 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
46
Wk7D2: How can amino acids produce glucose?
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
47
Wk7D2: What is used in the redox reactions in the conversion of amino acids?
NADH (reduced form) and NAD+ (oxidized form)
FADH and FAD+
Energy is being used.
48
WK7D2: What is transamination used for?
It is important in the formation of nonessential amino acids thru enzymes known as aminotransferases
49
WK7D2: What other important biological molecules can be made from amino acids?
fatty acids (lipids)
50
WK8D2: Where is the major site of nucleotide metabolism?
metabolic requirements are based on dietary intake or they are synthesized from scratch (purines and pyrimidines)
Purines occurs in the liver
51
WK8D2: Where are purines synthesized?
Liver
52
WK9D1: Eicosanoids are derived from what?
Arachidonic acids
53
WK9D1: How are Leukotrienes and lipoxins synthesized and from what source?
Synthesized from arachidonic acids via the linear pathway (enzyme 5-lipoxygenase)
54
WK9D1: How are Prostaglandins and thromboxanes synthesized and from what source?
Synthesized from arachidonic acid via the cyclic pathway (enzyme PGS-cyclooxygenase)
55
WK9D1: How is the cyclic pathway initiated?
initiated thru the action of prostaglandins G/H synthase (prostaglandin endoperoxide synthase-PGS)
56
WK9D1: What two cyclooxygenases are both catalyze the 2-step conversion of arachidonic acid to PGG2 and then to PGH2?
COX-1 and COX-2
57
WK9D1: Which COX is inducible and expressed in macrophages and monocytes in response to inflammation?
COX-2
58
WK9D1: Which COX is expressed in gastric mucosa, kidney, platelets, and vascular endothelial cells?
COX-1
59
WK9D1: During the cyclic pathway the enzyme PGS possess two activities, what are they?
Cyclooxygenase and Peroxidase
60
WK9D1: How is the linear pathway initiated?
Initiated thru the action of LOX's (lipoxygenase)
61
WK9D1: How many parts can LOX (lipoxygenase) be divided into? What are they?
3 forms; 5-LOX, 12-LOX, and 15-LOX
62
WK9D1: Which LOX produces leukotrienes?
5-LOX
63
WK9D1: How do the inflammatory mediator elicit response?
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)
64
WK9D1: What other important roles do inflammatory mediators play a part in?
Inhibiting gastric acid secretion
Regulating blood pressure through vasodilation or vasoconstriction
inhibiting or activating platelet aggregation and thrombosis
65
WK9D1: What is a fever and what causes it?
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)
66
WK9D1: What are the 2 types of signals that tightly maintains temperature?
Peripheral nerves and temperature of the blood in the region
67
WK9D1: How tightly is the body temperature maintained?
Tightly maintained through a process that allows the body to maintain its core internal temperature called thermoregulation
68
WK9D1: What area of the body is responsible for thermoregulation?
Hypothalamus
69
Wk9D1: How does the body regulate the temp?
Body temp is regulated by the "set point of the hypothalamus"
70
WK9D1: How does the body lower its temperature? Give an examples
By vasodilation which leads to heat loss and sweating
71
WK9D1: How does the body raise its temperature?
By vasoconstriction which is first noticed in the hands and feet, causing a reduction in heat loss from the skin
72
WK9D1: What is an example of how the body raises its temp?
Shivering can induce body temperature to rise due to heat production in the muscles
73
WK9D1: What is Hyperthermia?
Uncontrolled increase in body temperature that exceeds the body's ability to lose heat
74
WK9D1: What is Hypothermia?
Occurs when the body loses heat and can't produce heat fast enough to compensate for the loss
75
WK9D1: What is the widely used class of drugs used to treat a fever?
NSAIDs
76
WK9D1: NSAIDs, indomethacin and phenylbutazone all act upon the cyclooxygenase activity by doing what?
Inihibiting both COX-1 and COX-2
77
WK9D1: What is arachidonic acid? Where is it found?
Polyunsaturated omega-6 fatty acid
Found in the liver, brain and glandular organs
78
WK9D1: What is phospholipase A2 and what role does it play in the production of arachidonic acid?
Phospholipase A2 (PLA2) is the key enzyme to initiate arachidonic cascade and eicosanoid production
79
WK9D1: A (20:4 cis D5, 8, 11, 14) is converted to what started by COX enzymes?
arachidonic acid is converted to prostaglandins and thromboxanes by COX enzymes
80
WK9D1: What is the difference between COX-1 and COX-2?
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
81
WK9D1: Why do drug companies target COXs with NSAIDs?
NSAIDs could inhibit the COX-1 and COX-2 and other drugs can't
82
WK9D1: A (20:4 cis D5, 8, 11, 14) is converted to what started by LOX enzymes?
arachidonic acid is converted to leukotrienes by the LOX enzymes known as lipoxygenase
83
WK9D1: Are these inflammatory mediators short or long acting? Why?
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.
84
WK9D1: What are some ways to bring down a fever?
NSAIDs, placing a damp towel on forehead, drinking fluids, lukewarm bath
85
WK9D1: What is defined a fever by clinicians?
100.4*F
86
WK9D1: When is a high body temperature not a fever? Be specific
Hyperthermia, which can lead to heat stroke (not regulated, body can no longer fight the increase in temp)
87
WK9D2: Where does the extrinsic and intrinsic pathways intersect?
Coagulation cascade
88
WK9D2: Name the 3 types of mechanisms that maintains hemostasis.
1. Vasoconstriction (vascular spasm)
2. Formation of platelet plug
3. Coagulation (blood clot)
89
WK9D2: Which pathways are involved when a blood clot is formed?
Intrinsic and extrinsic
90
WK9D2: What are the intrinsic and extrinsic pathways?
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)
91
WK9D1: Which NSAIDs are preferred for children?
Motrin or Tylenol
92
WK9D1: What are key regulatory points in the biosynthesis?
Eicosanoids are key mediators and regulators of inflammation and immunity
COX and LOX are inhibited because it's the rate-limiting step
93
WK9D1: How do the inflammatory mediators elicit the response?
Response is elicited by phagocytes releasing by cytokines and lipid messengers
94
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
```
B) Protease
95
WK9D2: What is the term that is used when the enzymes are inactive?
Zymogens
96
Wk9D2: All the humoral protein factors involved in the clotting cascade are secreted in the enzymatically active form.
True/False
False
97
Wk9D2: Platelets can only be activated by binding to collagen.
True/False
False
98
WK9D2: What are some other ways platelets can be activated?
Thrombin, ADP and Prostacyclin
99
WK9D2: The clotting cascade is a series of phosphorylation events to activate the proteins.
True/False
False
100
Wk9D2: Why do the numbers of the factors not go in order of their activation?
They are names in the order in which they were discovered
101
Wk9D2: What role do the endothelial cells play in the clotting cascade? Why is this important when it comes to vascular disease?
* increases calcium
* produce anticoagulants
* line the vessels inside and under the basement membrane
* acts as a barrier against activation
102
WK9D2: How does Coumadin inhibit clotting?
Inhibits vitamin K
| long acting ~12-14 hours
103
Wk9D2: What role in clotting do platelets play? Do they signal? If so how?
* 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
104
WK9D2: How does Heparin inhibit clotting?
Heparin inhibit thrombosis by inactivation activated Factor X and inhibiting the conversion of prothrombin to thrombin
105
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
```
B) X to Xa
"a" means it's activated
106
Wk9D2: Why is having a cascade more important than a single event?
Highly regulated, allows for localization/ very focal, allow for on-demand availability
107
WK9D2: What is the difference between hemostasis and thrombosis?
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
108
WK9D2: How is hemostasis initiated?
Hemostasis is initiated by blood vessel damage/cuts
109
WK9D2: How is thrombosis initiated?
Initiated by damaged to the endothelial lining of the blood vessel
110
WK9D2: What does hemostasis and thrombosis have in common?
Both lack nucleic acids, converge to form FACTOR Xa, same last 3 steps to stop blood loss
111
WK9D2: What type of enzymatic functions do the clotting factors possess?
Enzymatic cleavage
112
WK9D2: How is the enzymatic activity controlled? What is the termed used for these enzymes that are produce inactive and then activated enzymatically?
Zymogens are coagulation factors that are initially inactive but become activated when they are clipped by a serine protease
113
WK9D2: What must happen to fibrin to strengthen and stabilize the fibrin mesh?
Fibrin binds to platelets and stabilized the hemostatic plug
114
WK9D2: Which factor is involved when fibrin is used to be a stabilizer and strengthener?
Factor 13; cross links fibrin to stabilize clot
115
WK9D2: How does the clot break down and what is released?
Enzyme of plasmin is responsible for these conversions
* prothrombin to thrombin
* fibrin to fibrinogen
* plasminogen to plasmin
116
WK9D2: What are the 3 steps that hemostasis and thrombosis share?
1) platelet bind to collagen, platelet plug formation
2) Formation of fibrin mesh, clot formation/coagulation
3) plasmin dissolves the clot
117
WK9D2: What is the coagulation pathway and what are the factors involved?
Coagulation pathway forms thrombin, it's the process by which blood forms clots.
May coagulation factors are zymogens pf serine proteases
118
WK9D2: How are the intrinsic and extrinsic pathways regulated?
it goes from inactive to activated by zymogens that cleave enzymes giving it a short half life
119
WK9D2: What are the consequences when one of the factors is missing?
Example
Impaired ability for blood to coagulate which can lead to excessive bleeding.
Hemophilia A & B
120
WK9D2: What type of enzymes are involved in the cascade? How is this important?
Zymogens of serine protease
Coagulation factors that become activated then inactivated during the overall process
121
WK9D2: What are t-PA and streptokinase and what are they used for?
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
WK9D2: What role does collagen play in platelet aggregation?
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
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
True
124
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
E) none of the above
125
```
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-
```
A) Fe2+
126
WK10D1: Myoglobin binds O2 with the same affinity and carries it to the muscle in the RBC like hemoglobin.
True/False
False
* Myoglobin has a higher affinity
* in the muscles
* hyperbolic function
127
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+
B) the left of the adult hemoglobin indicating higher affinity for O2.
128
WK10D1: Under what conditions (physiologically) would you not saturate the hemoglobin in the lungs?
In high altitude
129
WK10D1: How is CO2 carried back to the lungs from the tissues where it is produced? What enzymes is involved?
CO2 binds to hemoglobin, some turns into hydrogen bicarbonate.
enzyme: carbonic anhydrase
130
WK10D1: How does hemoglobin act as a buffer?
Stabilized T state; take up H+ proton in kreb cycle and respiratory system
131
WK10D1: How does this mutation cause the "sickling" shape of the RBC under what condition?
* 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
WK10D1: What are the physiological consequences of the sickle shape?
Hypoxia --> brain
sickle cells can get stuck and block blood flow --> pain and infection
133
WK10D2: How are chromosome abnormalities analyzed and what methods are used?
!) Standard cytogenetic analysis
2) Molecular cytogenetics
3) Array-based methodologies (cytogenomics)
4) Next-Generation Sequencing- Based methodologies
134
WK10D2: How do the methods work to analyze the abnormalities?
Probes, fluorescence and scanning
135
WK10D2: What types of chromosome abnormalities take place?
1) Numerical chromosome abnormalities
| 2) structural chromosome abnormalities
136
WK10D2: What are the 5 different structural abnormalities?
1) Deletions
2) Duplications
3) Translocation
4) Inversions
5) Uniparental Disomy
137
WK10D2 (Structural chromosome abnormalities): Loss of chromosomal segment
Deletions
138
WK10D2 (Structural chromosome abnormalities): inheritance of a pair of chromosomes from only one parent
Uniparental disomy
139
WK10D2 (Structural chromosome abnormalities): exchange of chromosomal segments between at least 2 chromosomes
translocations
140
WK10D2 (Structural chromosome abnormalities): rearranged segment, where there are two breaks within a chromosome, with the intervening chromosomal material inserted in an inverted orientation
inversions
141
WK10D2: How do the chromosome abnormalities take place?
Cell replication occurs in mitosis and meiosis (meiosis is an inherited trait) which is where chromosome abnormalities can occur (in metaphase)
142
WK10D2: How can chromosome abnormalities cause cancer?
Fusing protein: turning 2 proteins on together that shouldn't be together
143
WK10D2: Errors in mitosis are what leads to an extra chromosome being passed onto the child.
True/False
False
Correct answer: Meiosis
144
WK10D2: An individual can not survive if they have an extra chromosome.
True/False
False
Example: Down Syndrome - Chromosome 21
145
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
```
D) Protein sequencing
DNA being sequencing and gets mutated not proteins
146
WK10D2: Maternal age is a factor in developing chromosome abnormalities.
True/False
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
WK10D2: Aneuploidy is best described as the loss or gain of a chromosome.
True/False
True
148
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.
Mosaicism
149
WK10D2: This is a type of numerical chromosome abnormality that takes place when there are an extra or missing chromosome.
Aneuploidy
150
WK10D2: An example of aneuploidy is:
Down Syndrome
151
WK10D2: An example of mosaicism is:
Turner Syndrome
152
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
Chromosome Banding
153
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
Standard Cytogenetic analysis
154
WK10D2: (Type of method used to analyze chromosome abnormalities): links chromosome and molecular analysis as well as overcome some limitations of standard cytogenetics
molecular cytogenetics
155
WK10D2: FISH is an example of which type of method used to analyze chromosome abnormalities?
Molecular Cytogenetics
156
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.
FISH Fluorescence in situ Hybridization
157
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
Array-based methodologies
158
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
next generation sequencing
159
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
Trisomy 13
160
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
Trisomy 18
161
WK10D2: How can chromosome abnormalities cause cancer?
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
WK10D2: When would the chromosome abnormality be fix in the genetics and passed on?
Meiosis: sex cell replication
from diploid to haploid
allows for chromosome recombination
163
WK10D2: How do you analyze the changes in chromosome aberrations?
Small to large or large to small
Large to small
164
WK11D1: How is DNA packages in the eukaryotic cell?
Chromatins made up of condensed DNA (histones)
165
WK11D1: What levels of packing are achieved?
* Naked Double-helical DNA
* Fibril of nucleosomes
* chromatin fiber of super helical nucleosomes
* condensed metaphase chromosome loops
166
WK11D1: What proteins allow this packing to happen?
Nucleosomes
H2A and H2B
H3 and H4
167
WK11D1: Which types of histones form dimers?
H2A and H2B
168
WK11D1: Which types of histones form tetramers?
H3 and H4
169
WK11D1: What are nucleosomes?
composed of DNA wound around an octameric complex of histone molecules
170
WK11D1: What are the 4 major types of histones?
H2A
H2B
H3
H4
171
WK11D1: How is a chromosome described structurally?
Two-fold symmetry
172
WK11D1: What are the parts of a chromosome?
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
WK11D1: What does the noncondensed loops consist of?
Chromatin fibrils composed of nucleosomes
174
WK11D1: How are genes arranged on chromosomes?
1) Active
2) Inactive
3) Constitutive
4) Facultative
175
WK11D1: (Arrangement on chromosomes definitions): densely packed during interphase; heterochromatin
Inactive
176
WK11D1: (Arrangement on chromosomes definitions):always condensed and found near the centromere and telomeres
constitutive
177
WK11D1: (Arrangement on chromosomes definitions): at times is condensed while other times is inactive (transcribing)
facultative
178
WK11D1: (Arrangement on chromosomes definitions): large region that are more sensitive to digestion by nuclease; euchromatin
active
179
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
Indels
180
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
Recombination
181
Wk11D1: What is a jumping DNA and how is it important to gene expression?
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
Wk11D1: How does DNA replication initiate and where?
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
Wk11D1: What protein classes are involved in DNA replication?
```
DNA polymerase
Topoisomerase
Helicase
DNA Primase
Single-stranded binding protein
DNA Ligases
```
184
Wk11D1: Which protein class initiates synthesis of RNA primers?
DNA Primase
185
Wk11D1: Which protein class seals single strand nick between nascent chain and Okazaki fragments on lagging strand?
DNA Ligase
186
Wk11D1: Which protein is ATP-driven by unwinding of DNA?
Helicase
187
Wk11D1: Which protein class relieves torsional strain that is caused by helicase unwinding?
Topioisomerase
188
Wk11D1: Which protein prevents premature hardening of ssDNA that leads to dsDNA?
Singe-stranded Binding Protein
189
Wk11D1: Which protein is deoxynucleotide polymerization?
DNA polymerase
190
Wk11D1: What steps must take place for DNA to replicate?
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
Wk11D1: What is a replication bubble?
an unwound and open region of a DNA helix when DNA replication occurs
192
Wk11D1: What are leading and lagging strands?
Leading: DNA synthesis occurs continuously
Lagging: DNA synthesis occurs discontinuously in fragments
193
Wk11D1: What are the DNA fragments called and where do they occur?
Okazaki fragments on the lagging strand
194
Wk11D1: Why does leading and lagging strands occur?
The formation of leading and lagging strands allows for primase to be formed, allowing polymerase to begin synthesizing
195
Wk11D1: What types of damages can occur to DNA?
1) Single-base Alteration
2) Two-base Alteration
3) Chain Breaks
4) Cross-linkage
196
Wk11D1: What causes the damage in single-base alteration?
depurination: release of adenine or guanine
Deamination of cytosine to uracil
deamination of adenine to hypoxanthine
Alkylation of base
base analog incorporation
197
Wk11D1: What causes the damage in a two-base alteration?
1) UV light-induced thymine-thymine (pyrimidine) dimer
| 2) Bifunctional alkylating agent cross-linkage
198
Wk11D1: Ionizing radiation, radioactive disintegration of backbone element and oxidative free-radical formation cause which type of DNA damage?
Chain breaks
199
Wk11D1: what causes the damage in a cross-linkage?
1) between bases in same or opposite strands
| 2) between DNA and protein molecules (histones)
200
Wk11D1: What are ways that the different lesions can be repaired?
1) Mismatched repair
2) base excision repair
3) nucleotide excision repar
4) homologous recombination
5) nonhomologous end-joining
201
Wk11D1: The only enzyme involved in DNA replication is the DNA polymerase.
True/False
False
RNA transcriptase/DNA polymerase
DNA ligase
Helicase
Topoisomerase
202
Wk11D1: DNA is always enzymatically synthesized in the 5' to 3' direction.
True/False
True
203
Wk11D1: During DNA replication, the leading strand is made in fragments and the lagging strand is made continuously.
True/False
False
Leading: continuously
Lagging: fragments
204
Wk11D1: The only errors that can happen to the DNA sequence are caused by ionizing radiation.
True/False
False
long wave radiation
Base excision repair
bulking lesion
205
Wk11D1: Why is bulking lesions easier to recognize?
It's a dimer
206
Wk11D1: The double stranded DNA in a Eukaryotic cell is coiled around histones and looped into higher order structures to form chromosomes.
True/False
True
207
Wk11D1: What are the levels of DNA packaging?
1) Naked DNA
2) Beads-on-a-string
3) nucleosomes
4) non-condensed loops
5) condensed loops
6) metaphase chromosome
208
Wk11D1: Describe how nucleosomes and packing of the DNA can be used to regulate gene expression.
Inactive and active form
inactive- more densely packed
209
Wk11D1: Why is the origin of replication an AT rich sequence?
AT is less stable than a GC bond
210
Wk11D1: What problem must be overcome in the replication bubble?
conversion of RNA
211
Wk11D1: Both the leading and lagging strand synthesize in the 5' to 3' direction.
True/False
True
212
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
True
213
Wk11D1: DNA polymerase can add nucleotide only to the 3' end of the DNA strand.
True/False
True
214
Wk11D2: What is a promoter?
A distinct site on the DNA templates that enzymes attach to before the beginning of RNA synthesis.
215
Wk11D2: What is region where RNAP binds to DNA with a higher affinity?
Promoter region
216
Wk11D2: What are the transcription cycle steps?
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
Wk11D2: What transcribes the DNA into RNA?
RNA polymerase enzyme
218
Wk11D2: What are the classes of transcription factors involved in mRNA gene transcription?
1) Basal components
2) Coregulators
3) Activators
219
Wk11D2: What is termination and how does it happen?
Occurs when transcription comes to an end and RNA polymerase crosses a stop (termination) sequence in the gene
220
Wk11D2: What are the stop codons?
UAA
UAG
UGA
221
Wk11D2: What are the 2 mechanisms of termination?
1) Bacterial RNAP: can directly terminate transcription
| 2) Rho-factor-RNAP Interactions: lead to termination
222
Wk11D2: How is RNA processed?
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
Wk11D2: What is alternative splicing and what benefit is this to the cell?
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
Wk11D2: What other RNAs are in the cell besides mRNA?
rRNA -ribosomal
| tRNA- transfer RNA
225
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
True
I changed the original iRAT question.
(left to right --> bottom is template)
226
Wk11D2: All RNA in the cell is composed of mRNA.
True/False
False
rRNA
tRNA
227
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) Alternative splicing
(cutting up the same strand)
example: think about a train, mixing and matching different types of cargos and wagons
228
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) Transcription like replication proceeds in the 3’ to 5’ direction.
C) Splicing of mRNA takes place in the cytoplasm
229
WK11D2: What signaling pathways could activate or repress a gene? HOW?
GPCR signaling transduction pathway
- Calcitonin increase
- Vasopressin increase
- Dox decrease
- allosteric change during phosphorylation
230
WK11D2: What are the steps in the production of mRNA?
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
WK11D2: What is the potential consequence if an intron is not spliced out?
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
Define Aggregation
Formation of a number of things into a cluster
aka "cluster formation"
233
Review: What would be the best and most energy efficient way to interconvert the nucleotides?
Make triphosphates from monophosphates
234
WK9D2: What are the 3 types of clots (thrombin) formed?
1) White thrombus
2) Red Thrombus
3) Fibrin deposits
235
WK9D2: What is a clot composed of and how does it form? How is a clot dissolved?
Clots are composed of fibrinogen which is converted to fibrin by thrombin.
degraded by serine protease known as plasmin
236
WK9D2: Coagulation Factors include
```
VIII (8)
IX (9)
X (10) * V (5)
XI (11)
XII (12)
prothrombin
```
237
WK9D2: Factor VIII deficiency results in
hemophilia A (X-linked)
238
WK9D2: Factor IX deficiency results in
hemophilia B (X-linked)
239
WK9D2: Factor XI deficiency results in
hemophilia C
240
WK9D2: What is the most common hereditary bleeding disorder?
von Willebrand disease results in a deficiency of von Willebrand Factor
241
WK9D2: Which type of enzyme leads to conversion of fibrinogen to fibrin monomers in the cascade?
Thrombin
242
WK9D2: Which lab test is used to measure the extrinsic pathway of coagulation, thrombosis and platelet aggregation?
Prothrombin time
also measures effectiveness of warfarin
243
WK9D2: Which lab test is used to measure the intrinsic pathway of coagulation, thrombosis, and platelet aggregation?
Activated partial thromboplastin time
also monitors heparin therapy
244
WK1D1: ALL transport of molecules into or out of the cell require energy in the form of ATP.
True/False
False
245
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
False
246
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) DNA
B) Carbohydrates
C) Lipids
D) Amino acids
247
WK1D1: Like bacteria, Human Eukaryotic cells have membranes and cell walls to provide for structural integrity and rigidity.
True/False
False
248
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
False
Another transporter: sodium-potassium pump. ABC family transporter
249
WK1D2: A membrane channel or pore can ONLY more molecules in one-direction.
True/False
False
pore is a hole in a cell membrane made a specific protein to allow certain substances and dictate what could pass
250
WK1D2: Characteristics which affect the diffusion of a molecule across the membrane are?
A) Hydrophobicity
B) Charge
C) Size
D) All of the above
D) All of the above
251
WK1D2: Proteins which are associated and not integrated with the outer membrane are primarily interacting with the hydrophobic tails of the membrane.
True/False
False
The hydrophobic tails are on the inside.
252
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
True
253
WK2D2: Components of the extracellular matrix contains proteins and can also contain carbohydrate.
True/False
True
254
WK2D2: Collagen Type 2 is the only component of the extracellular matrix.
True/False
False
Collagen I - bone
Collagen II - cartilage
255
WK2D2: ALL receptors involved in signaling are integrated into the plasma membrane.
True/False
False
some are peripheral; steroid receptors go to the nucleus
256
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) Tyrosine
B) Serine
C) Threonine
257
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
```
E) None of the above
258
WK3D1: More than one signaling pathway can be integrated to lead to a cellular response.
True/False
True
GPCR
259
WK3D1: Which item below would be a common theme amongst the signaling pathways?
```
A) PO4
B) SO4
C) AMP
D) ATP
E) ADP
```
A) PO4
GDP (inactive)
--hydrolyze -->
GTP (active)
GDP + PO4 = GTP
260
WK3D1: GPCR are made up of multiple subunits besides the seven membrane spanning regions.
True/False
True
Tyrosine kinase dimerization
261
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
False
Negative response (down regulation)
Positive response
(up regulation)
262
WK3D2: The reason chemotherapy works so well on cancer cells is because they are in the G0 phase of cell cycle.
True/False
False
G0 - rapidly growing cells
Most radiosensitive - G1 & M phase
263
WK3D2: Which item below is NOT associated with the cell cycle?
```
A) CDK
B) Cyclins
C) Checkpoints
D) Phosphorylation
E) GDP
```
E) GDP
264
WK3D2: Most cells in the body typically "hang out" in G0 phase of the cell cycle.
True/False
True
265
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
```
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
WK3D2: The cell cycle is a disorganized random series of evens when a cell undergoes cellular division.
True/False
False
267
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) Mitochondria
268
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) Caspase-protease
269
WK4D1: Apoptosis and necrosis both result in cell death with the same outcome that the cell is phagocytosed to minimize inflammation.
True/False
False
270
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) Tightly regulated
271
WK5D1: Which item(s) listed below are involved in metabolism?
```
A) Organs
B) Cells
C) Blood
D) Mitochondria
E) All of the above
```
E) All of the above
272
WK5D1: Catabolism is the process of breaking down complex molecules to simple molecules and energy production.
True/False
True
CO2, Water, NH3
273
WK5D1: The cell can produce energy from only lipids.
True/False
False
Carbohydrate - cellulose
Proteins- glucose
274
WK5D1: Metabolism consists of only catabolism.
True/False
False
Anabolism - building of small molecules into complex ones
275
WK5D2: Inhibitors of enzymes reactions inhibit by one mechanism only.
True/False
False
Competitive and noncompetitive
276
WK5D2: Enzyme reactions only go in one direction (substrate to product).
True/False
False
277
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) Amount in (liters) -> Km
