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Flashcards in Biochemistry. Just kill me now. Deck (154)
1

mRNA start codon:

AUG
AUG AUGments protein synthesis

2

What does AUG code for in prokaryotes?
Eukaryotes?

Prokaryotes = formylmethionine
Eukaryotes = methionine

3

mRNA stop codons (3):

UGA
UAA
UAG
U Go Away, U Are Away, U Are Gone

4

What is an operon (3 components)?

Structural genes to be transcribed
Regulatory regions
Promoter region

5

Four common structural features shared by proteins that interact with DNA:

helix-loop-helix
helix-turn-helix
Zn fingers
leucine zippers

6

What are the three types of RNA?

rRNA
mRNA
tRNA
Rampant, massive, and tiny.

7

T/F: Enhancers and repressors control whether a gene is transcribed.

F. Response elements control the RATE of transcription, not whether it happens.

8

Features of promoter sequences (3):

Upstream
Rich in AT
TATA or CAAT box

9

What is an operator region?

It is where inducers and repressors bind, usually located between the promoter region and start.

10

Briefly review the function of the lac operon.
- Transcription factor
- Repressor
- Conditions

lac = codes for b-galactosidase (lactose -> glucose + galactose).
Tx factor CAP is bound when there is no glucose.
Repressor lac is bound when there is no lactose.
Make product only when the repressor is gone (there is lactose) and when CAP is unbound (there is glucose).

11

What are the three eukaryotic RNA polymerases and what do they do?

RNA pol I makes rRNA
RNA pol II makes mRNA
RNA pol III makes tRNA

12

This substance inhibits eukaryotic RNA polymerase II:
Main manifestation of its toxicity?

a-amanitin.
Hepatotoxic.

13

The two ways in which transcription can be terminated in prokaryotes:

rho-dependent ATPase
rho-indepedent (GC-rich hairpin turn followed by a weak point rich in UUUUUUfall right off)

14

T/F: Prokaryotes have more than one polymerase:

F. They just have the one, it makes all three kinds of RNA.

15

Drug that inhibits prokaryotic RNA polymerase and turns your pee red:

Rifampin

16

Where is rRNA made?
mRNA?
tRNA?

rRNA is made in the nucleolus.
mRNA and tRNA are made in the nucleoplasm.

17

Before RNA leaves the nucleus it needs to be processed to become mRNA and gain the ability to leave. Three major processing events:

1. 5' cap addition (SAM needed)
2. Poly-A tail
3. Introns spliced out (by spliceosome)

18

What is the co-factor required for adding a 5' cap to hnRNA?

SAM

19

Poly-A polymerase recognizes this polyadenylation signal:

AAUAAA

20

Patients with lupus make antibodies against this piece of pre-mRNA processing machinery:

Spliceosomal snRNPs.
These are part of the spliceosome used to remove introns.

21

Which part of a transcript gets to leave the nucleus: Intron or exon?

EXon is EXpressed and EXits the nucleus

22

Does tRNA synthetase work at the 5' or 3' end of tRNA? What special marker is at this end?

tRNA synthetase works at the 3' end.
This end always has CCA.

23

T/F: Amino acids destined for transfer are bound hydrostatically to the 5' end of tRNA.

F. The bond is covalent, and it is found at the 3' end.

24

The ribosome in prokaryotes is a __S ribosome composed of these two subunits:

30S + 50S -> 70S
PrOkaryotic = Odd numbers

25

The ribosome in eukaryotes is a __S ribosome composed of these two subunits:

40S + 60S -> 80S
Eukaryotic = Even numbers

26

Where is the prokaryotic ribozme?

It is a 23S rRNA Inside the 50S subunit.

27

tRNA bound with ATP is in what state?
tRNA bound with GTP is in what state?

ATP bound tRNA is "charged" with its amino acid.
GTP bound tRNA is in the process of translocation.

28

Initiation of protein synthesis is activated by this hydrolytic reaction:

GTP hydrolysis

29

This enzyme catalyzes peptide bond formation during protein synthesis. It has two names:

Ribozyme = peptidyltransferase

30

Where are ribosomes made?

In the nucleus.

31

In order to accomplish translocation during protein synthesis, this protein is required in eukaryotes. What is its prokaryotic analogue?

Eukaryotic: EF-2
Prokaryotic: EF-G

32

In eukaryotes, which ribosomal subunit docks with mRNA first?
This subunit needs help, what proteins help it dock?

40S binds first with the help of initiation factors

33

Describe the orientation of the entrance and exit sites for peptide bond formation on the 60S subunit:

A site is near the 3' end, for Aminoacyl-tRNA.
P site is in the middle, for the growing Peptide.
E site is at the end, it holds Empty tRNA Exiting.

34

These antibiotics inhibit initiation complex formation and cause mRNA mis-reading:

Aminoglycosides

35

These antibiotics bind the 30S subunit of prokaryotic ribosomes and keep tRNA out of the A site:

Tetracyclines
prevent *t*RNA from binding

36

Two antibiotics that work at the 30S subunit:

Aminoglycosides
Tetracyclines
buy AT 30
CCELL at 50

37

These 6 antibiotics work at the 50S subunit of the ribosome:

Chloramphenicol
Clindamycin
Erythromycin (& other macrolides)
Linezolid
Lincomycin
Streptogramin

38

These antibiotic binds the 50S su and inhibit peptidyltransferase (2).
This antibiotic binds the 30S su and inhibits tRNA docking.

Chloramphenicol & streptogramins
Tetracyclines

39

Mechanism of action for macrolides, linezolid, and clindamycin:

Bind 50S and prevent the spent tRNA from leaving once it has donated its amino acid.

40

Mechanism of action of tetracyclines:

Bind 30S and block tRNA from entering the A.
Tetracyclines are not good for babies.

41

How do aminoglycosides work?

They bind the 30S subunit and inhibit initiation complex formation.

42

T/F: Cyclin-dependent kinases are constitutively inactive.

T. They need cyclins to activate them.

43

Two important tumor suppressors at the G0 to S transition in the cell cycle:

p53
Rb

44

What kind of cells are exemplified by bone marrow, skin, and other germ cells?

Labile cells

45

Hepatocytes and lymphocytes are capable of entering G1 when prompted, these cells are known as:

Stable or quiescent cells

46

These cells remain in G0. Regeneration happens from stem cells:
Examples (3)?

Permanent cells.
Ex neurons, skeletal / cardiac muscle, RBCs

47

rER in neurons is aka:
You would not see this substance in what portion of the neuron?

Nissl substance.
Nissl bodies are absent from axons

48

What happens in rER (2 big things)?

1. Synthesis of exported proteins
2. Addition of N-linked oligosaccharides

49

What happens in smooth ER?

1. Steroid synthesis
2. Detoxification of drugs and poisons

50

This cellular organelle will be enormous in people sniffing a lot of glue:

Smooth ER

51

The golgi has 5 main jobs:

1. Distribution center
2. Modifies N-linked oligosaccharides
3. Adds O-oligosaccharides
4. Adds M-6-P
5. Forms proteoglycans / sulfates sugars

52

N-linked oligosaccharides are modified on which amino acid? in which organelle does this happen? In what organelle were they added to a protein in the first place?

Asparagine
Golgi
rER

53

O-linked oligosaccharides are modified by the golgi on two amino acids:

Serine
Threonine

54

What happens if mannose-6-phosphate is not added to certain proteins in the golgi?

I-cell disease = inclusion cell disease. M-6-P targets proteins to the lysosome. No M-6-P = proteins leave the cell instead of going to the lysosome.

55

What is the enzyme that adds M-6-P to lysosome proteins in the golgi?

Phosphotransferase.

56

Three features of I cell disease:

Coarse facies
Clouded corneas
Restricted joint movement...
2/2 high levels of lysosomal enzymes

57

This organelle catabolizes very long chain fatty acids and amino acids:

Peroxisome

58

Three modes of protein degradation:

1. Ubiquitin-dependent (in a proteasome)
2. Lysosomal
3. Calcium-dependent cytosolic enzymes

59

What is the cause of I cell disease?

Deficiency in M-6-P leading to defective trafficking of lysosomal-bound proteins and excretion.

60

5 drugs that act on microtubules:

Mebendazole / thiabendazole (for BENDy worms)
Griseofulvin
Vincristine / vinblastine
Paclitaxel
Colchicine

61

What does Chediak-Higashi syndrome have to do with microtubules?

LYST = mutated lysosome traffic regulator gene. Needed for microtubule-dependent sorting of endosomal proteins into late endosomes.

62

This protein is responsible for retrograde movement down the micrtubule.
This one is responsible for anterograde.

Dynein (moves from assembing end to assembling end).
Kinesin

63

Characteristic arrangement of microtubules in a cilum:

9+2

64

Defect found in Kartagener's syndrome:

Immotile cilia
Defect is in the dynein arm.

65

Connective tissue can be identified by this immunohistochemical stain:

Vimentin

66

Muscle can be identified by this immunohistochemical stain:

Desmin

67

Epithelial cells can be identified by this immunohistochemical stain:

Cytokeratin

68

Neuroglia can be identified by this immunohistochemical stain:

GFAP identifies neuroGlia

69

This immunohistochemical stain identifies Neurons:

Neurofilament stain

70

This immunohistochemical stain can be used to identify adrenal neuroblastoma:

Neurofilament

71

This immunohistochemical stain can be used to identify astrocytomas:

GFAP

72

Cilia use this organizational feature to coodinate contraction:

Gap junctions

73

This drug inhibits the Na+/K+ ATPase by binding to the K+ site:

Ouabain

74

Drug that inhibits the Na+/K+ ATPase directly:

Digoxin / digitoxin

75

Type of collagen defective in OI:

Type I

76

Type of collagen most frequently defective in Ehlers-Danlos:

Type III

77

Type of collagen defective in Alport syndrome:

Type IV

78

Where would you find Type I collagen?

Bone
Skin
Tendons

79

Where would you find Type II collagen?

Cartilage

80

Where would you find Type III collagen?

Reticulin-containing organs:
Skin
Blood vessels
Uterus / fetal tissue
Granulation tissue

81

Where would you find Type IV collagen?

Basement membrane

82

Collagen synthesis begins with this molecule:

Pre-pro-collagen

83

Hydroxylation of pre-pro-collagen requires this vitamin:

Vitamin C

84

Deficiency in vitamin C leads to a defect at which point in the synthesis of collagen?

Hydroxylation of pre-pro-collagen at lysine and proline residues.

85

What is procollagen made of?

Glycosylated hydroxylysine residues wound in a triple helix.

86

What structural feature of pro-collagen is distorted in osteogenesis imperfecta?

Triple helix

87

Problems with cross-linking tropocollagen lead to this inherited connective tissue disease:

Ehlers-Danlos

88

Mode of inheritence of OI:

Autosomal dominant

89

Four very common presenting features of OI:

1. Multiple fractures, minimal trauma
2. Blue sclerae
3. Hearing loss
4. Dental problems due to lack of dentin

90

What is the defect in Alport syndrome?

Type IV collagen

91

Most common mode of inheritence for Alport syndrome:

X-linked recessive

92

Three common features of Alport syndrome:

1. Progressive hereditary nephritis
2. Deafness
3. Lenticonus = thinning of capsule around lens
"Can't SEE, can't PEE, can't HEAR me."

93

Enzyme that breaks down elastin?
Protein that inhibits this enzyme?

Elastase
a1-antitrypsin

94

Emphysema in a young non-smoker, think:

a1-antitrypsin deficiency

95

Marfan's syndrome is caused by a defect in this protein. What is its function?

Fibrillin.
Function is to be the "scaffold" for tropoelastin in elastin formation.

96

In what tissues is elastin particularly important?

Blood vessels
Alveoli
Larynx
Spine

97

First step in the metabolism of alcohol is catalyzed by this enzyme:
Drug that inhibits this enzyme?

Alcohol dehydrogenase.
Fomepizole

98

The enzyme alcohol dehydrogenase is limited by this reagent:

NAD+

99

Enzyme that catalyzes acetaldehyde -> acetate in alcohol metabolism:
Drug that inhibits this enzyme?

Acetaldehyde dehydrogenase.
Antabuse

100

Antidote for methanol and ethylene glycol poisoning?

Fomepizole

101

Mechanism of action of antabuse:

Blocks acetaldehyde dehydrogenase, allows acetaldehyde to build up. Instant hang-over.

102

Explain the mechanism behind ethanol-induced hypoglycemia (5 steps):

1. NADH/NAD+ ratio is increased (need NAD+ to metabolize alcohol)
2. Detoxifying = more important than gluconeogenesis, so pyruvate -> lactate and OAA -> malate to generate NAD+ for detox.
3. TCA cycle shuts down, depletion of OAA.
4. Acetyl CoA -> ketone production, not gluconeo.
5. Malate -> NADPH -> FA synthesis.

103

Severe protein malnutrition is aka:
Four big signs:

Kwashiorkor
Malnutrition (skin lesions, hypopigmentation)
Edema (protein holds water in place)
Anemia
Liver is fatty (can't make apoB100, fats can't leave liver)

104

Energy malnutrition is aka:

Marasmus

105

Rate-limiting enzyme for glycolysis:

Phosphofructokinase-1
= PFK-1

106

Rate-limiting enzyme for gluconeogenesis:

Fructose-1,6-bisphosphatase

107

Rate-limiting enzyme for glycogen synthesis:

Glycogen synthase

108

Rate-limiting enzyme for glycogenolysis:

Glycogen phosphorylase

109

This enzyme is responsible for trapping glucose in the cell:
Version in the liver and glucose-regulating cells? Version in skeletal muscle and adipose?

Glucokinase
LIver cells have glucokinase
Adipose / skeletal muscle cells have hexokinase

110

Enzyme responsible for glucose-6-phosphate release from the cell as glucose:

Glucose-6-phosphatase

111

Enzyme responsible for generating pyruvate:

Pyruvate kinase

112

Enzyme responsible for converting pyruvate to oxaloacetate:

Pyruvate carboxylase

113

Enzyme that sends pyruvate into the TCA cycle:
5 co-factors required to do this:

Pyruvate dehydrogenase
Makes Acetyl-CoA from pyruvate
Thiamine (B1)
Lipoic acid
CoA (B5)
FAD (B2)
NAD (B3 = niacin)

114

Main presenting feature of glycolytic enzyme disease:

RBC cannot maintain their Na/K-ATPase -> hemolytic anemia.

115

Most common glycolytic enzyme deficiency:

Pyruvate kinase deficiency

116

Pyruvate has four major fates. What are they, and what is the rate-limiting enzyme that takes it down that path?

1. Alanine cycle (ALT)
2. Cori cycle (make lactate, LDH)
3. TCA cycle (PDH, make acetylCoA)
4. Oxaloacetate (Gluconeogenesis, P.carboxylase)

117

Three main features of arsenic poisoning:

Garlic breath
Vomiting
Rice water stool

118

Pyruvate dehydrogenase deficiency can come about in three ways:

Congenital (X-linked)
Acquired (arsenic poisoning, vitamin deficiency)

119

Pyruvate dehydrogenase deficiency results in this major metabolic disturbance. Why?

Lactic acidosis, this is because pyruvate can't enter the TCA cycle, so it builds and gets shunted down the Cori cycle.

120

Treatment of pyruvate dehydrogenase deficiency:

High fat diet
Lysine and Leucine onLy pureLy ketogenic amino acids

121

Vitamin deficiencies that can lead to pyruvate dehydrogenase deficiency:

Thiamine (B1)
Lipoic acid (remember arsenic messes this one up)
CoA (B5)
FAD (B2)
NAD (B3, niacin)

122

Enzyme that starts the Kreb cycle:

Citrate synthetase

123

Substances that inhibit Complex I of the ETC (3):

Amytal (barbiturate)
Rotenone (fish poison)
MPP (from MPTP, of home opiate lab fame)

124

This substance inhibits Complex III of the ETC:

Antimycin A

125

These substances inhibit Complex IV of the ETC (4):

CN
CO
H2S
N3 (sodium azide)

126

This substance inhibits Complex IV of the ETC, aka the ATP synthase:

Oligomycin

127

Name as many substances that are wrenches in the ETC as you can:

Rotenone
Amytal
MPP
Antimycin A
CN
CO
N3-
H2S

128

What is the goal, overall, in simplistic terms, of the ETC?

1. Send NADH electrons down a chain of molecules.
2. Build high H+ concentration in the intermembranous space, use it to drive ATP production in the mitochondrial matrix.
3. Final acceptor = water.

129

What is the mechanism of action of oligomycin?

It directly inhibits ATP synthesis.

130

What is an uncoupling agent?
Can you name 3?

Something that increases the permeability of the mitochondrial inner membrane. This causes consumption of oxygen and dissipation of heat.
2,4-DNP, aspirin, thermogenin

131

Why can't muscle do gluconeogenesis?

It does not have glucose-6-phosphatase, can't release glucose.

132

T/F: Even chain fatty acids can serve as a glucose source.

F. They can only make acetyl-CoA. Odd chain FA yield propionyl-CoA, which can go into the TCA cycle.

133

What are the four irreversible enzymes of gluconeogenesis?

Pathway Produces Fresh Glucose:
Pyruvate carboxylase
PEP carboxykinase
Fructose-1,6-bisphosphatase
Glucose-6-phosphatase

134

What five really huge things do you need NADPH for?

Needed for reductive reactions:
1. Making fatty acids / cholesterol
2. Making O2 free radicals
3. Protecthing RBCs from free radicals
4. In the CYP450 system
Also needed for:
5. Ribose (nucleotide synthesis)

135

Which tissues in the body use the pentose phosphate pathway?

Lactating mammary glands
Liver
Adrenal cortex (... anything making fatty acids / steroids)
RBCs (reducing, protect themselves)

136

Three important enzymes in respiratory burst and what each makes:

NADPH oxidase (makes O2 free radicals)
SOD (makes H2O2)
Myeloperoxidase (makes HoCl)

137

NADPH oxidase deficiency results in this immune deficiency disease:

Chronic granulomatous disease

138

What is the overall purpose of the HMP shunt (aka pentose phosphate pathway)?

Make NADPH from G-6-P.
NADPH = used in reductive reactions.

139

Think of this as the body's endogenous anti-oxidant when it is in its reduced form:

Glutathione

140

Enzyme defect that leads to an inability to keep glutathione reduced:

G-6-P deficiency, these cells have no NADPH to help them.

141

Mode of inheritence of G-6-P deficiency:

X-linked recessive

142

Two features of RBCs in someone with G-6-P deficiency:

Heinz bodies = oxidized Hb
Bite cells

143

Pathogenesis behind G-6-P deficiency:

Low NADPH in RBC -> hemolytic anemia especially in the presence of oxidizing agents

144

Name 5 things that can precipitate massive hemolysis in someone with G-6-P deficiency:

Infection
TB drugs
Sulfonamides
Fava beans
Primaquine

145

The milder disorder of fructose metabolism:

Essential fructosuria

146

Deficiency of aldolase B:
What does it cause?

Fructose intolerance. Fructose -> fructose-1-phosphate eats up available phosphate. Glycogenolysis and gluconeogenesis are both inhibited.

147

Symptoms of fructose intolerance:

Vomiting
Hypoglycemia
Cirrhosis
Jaundice

148

Symptoms of essential fructosuria:

Mild diuresis on high intake, otherwise none.

149

Enzyme deficient in essential fructosuria?
In fructose intolerance?

Essential fructosuria = fructokinase
Fructose intolerance = aldolase B (FAB)

150

Two disorders of sugar metabolism that can cause infantile cataracts:
Which is the more severe?

Galactokinase deficiency
Galactosemia *

151

Substance that accumulates in galactokinase deficiency:

Glactitol

152

Enzyme defective in classic galactosemia:
T/F: This enzyme is used earlier in galactose metabolism than galactokinase, resulting in more severe disease.

Galactose-1-P uridyltransferase.
F. This enzyme is actually downstream, both galactose-1-P and galactitol build up -> cataracts, liver problems, mental retardation.

153

What is the action of insulin on protein kinase A and glycolysis?

INsulin INactivates glycogenolysis.

154

Epinephrine and glucagon share this action on protein kinase A

They both increase cAMP and activate protein kinase A