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Bio 3100 > Phase 4 > Flashcards

Phase 4 Flashcards

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1
Q

Which organs are responsible for destroying excess amino acids?

A

Kidney and Liver

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2
Q

What is the half life of the longest living protein and where is it located?

A

10 days and it is in the muscle

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3
Q

What are the two sources of protein?

A

Intracellular and dietary

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4
Q

What is NH4 removed by?

A

Aminotransferase

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5
Q

What are uricotelic animals?

A

Example: birds

Do not produce urea; produce uric acid

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6
Q

What are ammonotelic animals?

A

Example: fish

Dispose ammonia directly

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7
Q

What do we need to produce urea?

A

Water

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8
Q

What are urotelic animals?

A

Example: mammals

Produce urea

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9
Q

What is the main transporter of ammonia from the muscles?

A

Alanine

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10
Q

What is the main transporter of ammonia from tissues?

A

Glutamine

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11
Q

What do mosquitoes depend on?

A

The consumption of sugar

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12
Q

What is the water we ingest used for?

A

For producing urea

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13
Q

What do we not need to ingest?

A

Fat

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14
Q

What is the difference between enzymes?

A

Their selectivity

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15
Q

What cofactor and enzyme does alpha ketoglutarate use to get converted to L-glutamate?

A

PLP (pyridoxal phosphate) is the cofactor and aminotransferase is the enzyme

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16
Q

What happens if you take excess vitamins?

A

Schiff bases are created everywhere and they are very reactive

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17
Q

What does pyridoxal phosphate have that allows it to be converted?

A

It has an aldehyde which the aminotransferase changes to a Schiff base (pyridoxamine phosphate)

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18
Q

What does the conversion of glutamate to alpha ketoglutarate release?

A

NH4 which can be converted to urea or uric acid or can stay as NH4

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19
Q

Where does glutamate in the liver come from?

A

Amino acids turn into alpha ketone acids (alpha ketoglutarate) which gets converted to glutamate via PLP or glutamine can enter directly from muscles and other tissues and be converted to glutamate. Alpha ketoglutarate can also come from the krebs cycle. Alanine can also be converted into glutamate

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20
Q

What happens when pyridoxal combines with the aminotransferase?

A

It attacks the epsilon lysine to form a schiff base

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21
Q

What does glutamate dehydrogenase use?

A

It can use NAD+ or NADP+

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22
Q

What happens via glutamate dehydrogenase?

A

A reduction occurs to form an intermediate between glutamate and alpha ketoglutarate

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23
Q

What is NADH used for generally?

A

Catabolism

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24
Q

What is NADPH used for generally?

A

Anabolism

Can be used for synthesis of fatty acids but not a very important source

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25
Q

What is NH4 in tissues converted to and how?

A

Glutamine by reacting with glutamate and getting transported to the liver through the bloodstream to regenerate glutamate

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26
Q

What happens to the fumarate generated in the Urea Cycle?

A

It can move to the Krebs Cycle. Remember it is converted to malate in the cytosol so it can move back into the mitochondria

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27
Q

Where does the Krebs Cycle occur?

A

Mitochondria

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28
Q

Where does the Urea Cycle occur?

A

Partially in the mitochondria but mostly in the cytosol

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29
Q

Where is urea from the urea cycle released?

A

Cytosol

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30
Q

How is aspartate converted to oxaloacetate or backwards?

A

Alpha ketoglutarate goes to glutamate or reverse

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31
Q

How is oxaloacetate converted to malate and back?

A

By using NADH to NAD+ or reverse

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32
Q

What is urea production regulated by?

A

By the amount of amino acids present and allosteric intervention of N-acetylglutamate

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33
Q

What does the ingestion of more protein mean?

A

More urea produced

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34
Q

What does a large amount of aminotransferases in urine mean?

A

We have too many amino acids and are ingesting too much protein

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35
Q

Which aa specifically is affected by ingesting more protein?

A

More glutamate produced

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36
Q

How does glutamate go to carbamoyl phosphate?

A

Glutamate to N-Acetylglutamate via N-Acetylglutamate synthase and releasing Co-A

N-Acetylglutamate to carbamoyl phosphate via carbamoyl phosphate synthetase I and 2ATP going to A ADP + Pi

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37
Q

What do ketogenic amino acids produce?

A

Ketone bodies via acetyl coA

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38
Q

What do glucogenic amino acids produce?

A

Glucose

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39
Q

What amino acids are solely ketogenic?

A

Leucine and Lysine

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40
Q

What are all of the ketogenic amino acids?

A 
Lysine
Leucine
Tyrptophan 
Tyrosine
Phenylalanine
Isoleucine
Threonine
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41
Q

What are the glucogenic amino acids?

A

All aa except lysine and leucine

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42
Q

Why do we have low pH in the stomach?

A

Due to hydrochloric acid

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43
Q

How do we ingest material?

A

Pepsinogen goes to pepsin (a Ser protease)

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44
Q

What are the 3 main degradative proteases?

A

Trypsin, pepsin, and chymotrypsin

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45
Q

What does pepsin do?

A

Breaks down proteins to polypeptides

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46
Q

What happens after pepsin acts?

A

The polypeptides move through the intestine where zymogens (active proteases) break down the rest of the material

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47
Q

What does the small intestinal wall do?

A

Absorbs amino acids

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48
Q

What does the movement of substances from the intestine to the intestinal epithelial require?

A

A glucose sodium symporter

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49
Q

What does the movement of substances from the intestinal epithelial to the blood require?

A

A 3Na+(out)/2K+(in) antiporter and a glucose uniporter (out)

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50
Q

Why is alanine used in the muscle more than glutamate?

A

Since pyruvate is produced in the muscle and does not go to krebs in the muscle

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51
Q

What happens to excess pyruvate?

A

Goes to lactic acid or it is converted to alanine via aminotransferase

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52
Q

Why does the heart not need alanine?

A

It uses different energy sources

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53
Q

What does every aminotransferase use as a cofactor?

A

PLP

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54
Q

Why do we need 2 units of ATP to go from glutamate to carbamoyl phosphate?

A

Bicarbonate requires one unit along with carbamoyl phosphate synthetase and the other phosphorylates carbamate

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55
Q

Where does glutamate for the urea cycle come from?

A

1) Extrahepatic tissues
2) Synthesis from alanine or other amino acids thru alpha ketoglutarate
3) Conversion of oxaloacetate to aspartate via aminotransferase and uses alpha ketoglutarate to move NH4 around

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56
Q

How does oxaloacetate enter and leave the mitochondria?

A

Leaves by being converted to aspartate and enters by being converted to malate

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57
Q

What is the most abundant aminotransferase?

A

ALS (alanine aminotransferase)

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58
Q

What happens if you consume too much water?

A

You lose electrolytes and pass out because they dissolve in the water

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59
Q

What happens to the Schiff base that is created by the reaction of PLP with epsilon lysine?

A

It becomes an electrophile that can be attacked by another amino acid such as alanine (attacks at the carbon)

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60
Q

What happens to the tetrahedral intermediate that is formed by the reaction of alanine with the Schiff base that is formed by the reaction of PLP and epsilon lysine?

A

It can form pyruvate by reacting with water or it can form pyridoxamine

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61
Q

What is an amino acid?

A

Any compound that contains a amino and acid group

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62
Q

Where is beta alanine used?

A

Coenzyme A

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63
Q

Where is carnosine found?

A

The muscle

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64
Q

What is carnosine composed of?

A

Beta alanine histidine

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65
Q

What is the function of carnosine?

A

Histidine has a pKa of 6.1 but carnosine has a pKa of 6.8 so it is used as a buffer in blood

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66
Q

What is an advantage of using beta alanine as opposed to alpha alanine?

A

It is not coded so you are not limited in the amount that you can make

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67
Q

What are the various functions of glutamate?

A 
Part of glutathione
Processing of Ammonia
Used as starting material for aa
Glycolysis
Serves in proteins as acid/base catalyst and nucleophile
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68
Q

How many essential amino acids are there?

A

9

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69
Q

What vitamin is used as an antioxidant and what group does it have?

A

Vitamin E

Has a phenol

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70
Q

What amino acids can move in and out of the cytosol freely into the mitochondria?

A

Orinthine and Citrulline

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71
Q

What is the first step of the urea cycle?

A

Formation of carbamoyl phosphate

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72
Q

What enzyme forms alpha ketoglutarate in the urea cycle?

A

Glutamate dehydrogenase

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73
Q

What enzyme forms carbamoyl phosphate from NH4 and what is used in that conversion?

A

Carbamoyl phosphate synthetase

HCO3 and 2 ATP to form 2 ADP + Pi

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74
Q

What does oxaloacetate get converted into to leave the mitochondria?
To enter?

A

Leave: Aspartate
Enter: Malate

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75
Q

Where are protons in relation to the mitochondria?

A

More protons in the intermembrane space than outside

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76
Q

What does ATP synthase allow for?

A

Facilitated diffusion because it is not a proton pump

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77
Q

What is the general purpose of the 4 complexes/proton pumps in the chemioosmotic theory?

A

To reduce the energy of the electrons to the proper amount so that they can form O2

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78
Q

In the chemioosmotic theory, what is energy from electron flow stored as?

A

Electrochemical potential

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79
Q

What happens when a proton enters ATP synthase?

A

It forces the synthase to move and brings ADP and Pi close together so that they have to react to form ATP

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80
Q

What is the process of the chemioosmotic theory in the mitochondria?

A

1) Reduced substrate donates electrons
2) Electron pumps H+ as electrons flows to O2
3) Energy of electron flow stored as electrochemical potential
4) ATP synthase uses electrochemical potential to synthesize ATP

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81
Q

What is the process of the chemioosmotic theory in the chloroplast?

A

1) Light converts H2O to good electron donor
2) electron carriers pump protons in as electrons flow to NADP+
3) Energy of electron flow stored as electrochemical potential
4) ATP synthase uses electrochemical potential to synthesize ATP

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82
Q

What is complex 1 known as and what is its shape?

A

NADH dehydrogenase

L-Shaped

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83
Q

Where are the electrons from complex 1 transferred to and how?

A

Transferred to complex 3 by CoQ

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84
Q

How many protons does complex 1 pump out?

A

4

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85
Q

How does complex 1 allow the protons out?

A

When NADH comes in, the conformation of complex 1 changes and allows the pores to open to let the protons out

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86
Q

What are the prosthetic groups of complex 1?

A

FMN and Fe-S

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87
Q

Why is FMN used in complex 1?

A

Fe-S can only take 1 electron at a time so NADH cannot transfer electrons directly to it

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88
Q

What is complex 2 known as and where do its electrons go?

A

Succinate dehydrogenase

Electrons go to CoQ

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89
Q

How many protons does complex 2 pump?

A

0

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90
Q

What are the prosthetic groups of complex 2?

A

FAD and Fe-S

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91
Q

How does FADH2 enter complex 2?

A

Via the reaction of succinate to fumarate

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92
Q

What are the characteristicsof CoQ?

A

Lipophilic
Benzoquinone linked to 10 isoprene units
Can transfer 2 electrons in one step via stable semiquinone intermediate

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93
Q

What is complex 3 known as and where do its electrons go?

A

Cytochrome C oxidoreductase

Electrons go to cytochrome C

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94
Q

What prosthetic groups does complex 3 have?

A

Hemes, Fe-S

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95
Q

What are the coppers of complex 3 held in place by?

A

Histidines

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96
Q

What should all cytochromes be associated with?

A

Heme proteins

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97
Q

How many protons does complex 3 pump?

A

4

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98
Q

What is complex 4 known as and how many protons does it pump?

A

Cytochrome oxidase

2

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99
Q

What are the prosthetic groups of complex 4?

A

CuA, CuB, Hemes

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100
Q

When you lower the energy of the electrons by moving through the complexes, what can be said about the oxidation state?

A

You are moving from low to high oxidation state

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101
Q

Through the whole respiratory system, how many protons does one NADH pump?

A

10

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102
Q

Through the whole respiratory system, how many protons does 1 FADH2 pump?

A

6

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103
Q

What happens in the chemioosmotic theory when there is too much oxygen?

A

It will react in CoQ to form superoxide which will react with proton to form hydroxyl radical that is highly unstable

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104
Q

What will the hydroxyl radical in the chemioosmotic theory do?

A

React with any hydrogen to make water

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105
Q

What does superoxide dismutase make?

A

H2O2 from superoxide

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106
Q

What does glutathione reductase aid in in the chemioosmotic theory?

A

It converts NADPH to NADH+

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107
Q

How do you increase the amount of superoxide dismutase?

A

Breathing (increasing amount of oxygen in the body)

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108
Q

How do you decrease your heart rate?

A

By dilating the arteries through exercise

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109
Q

Why are you warmer when you exercise?

A

You use the protons that are pumped to produce thermogenin

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110
Q

What type protein is ATP synthase and how can it be removed?

A

Integral protein that can be removed by detergent

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111
Q

What are the subunits of ATP synthase F1?

A

3 alpha and 3 beta

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112
Q

What are the two portions of ATP synthase?

A

F0 attached to membrane

F1 in the mitochondria

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113
Q

Where is the ATP present in ATP synthase?

A

In the beta subunits of F1

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114
Q

How many total protons are required to make APT synthase work?

A

9

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115
Q

How do you move electrons as NADH from outside to inside the mitochondria?

A

Convert oxaloacetate to malate using 1 NADH and malate dehydrogenase

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116
Q

How do you move electrons as NADH from inside to outside the mitochondria?

A

Convert oxaloacetate to aspartate via aspartate aminotransferase

117
Q

How does CO inhibit the respiratory chain?

A

Interferes in complex 4 by binding in place of oxygen and in hemoglobin

118
Q

How does CN inhibit the respiratory chain?

A

Binding in place of oxygen

119
Q

Where do barbiturates inhibit the respiratory chain?

A

Complex 1

120
Q

Why will a small amount of cyanide kill you immediately but a large amount will not?

A

Large amount overwhelms the system so it won’t reach the complex immediately

121
Q

What does the respiratory chain do overall?

A

Catalyzes the flow of electrons from low reduction potential carriers to high reduction potential carriers

122
Q

What are the electron carriers in the respiratory chain?

A

Flavoproteins contain FMN or FAD (I and II)
Iron sulfur proteins contain non-heme iron clusters like F-S or Fe4S4 (I, II, III)
Coenzyme Q
Cytochromes contain hemes (a, b, c)
2 and 3 contain 3 b-type
3 has c
4 has a and a3

123
Q

What is used to produce heme?

A

Succinate

124
Q

Why does the conversion of NADH to O2 have to be stepwise?

A

The energy changes are specific

125
Q

What are the energy changes in the conversion of NADH to O2?

A

NADH -> FMN -69.5 kJ/mol
CoQ -> cytB -36.7 kJ/mol
Cyta -> O2 -112 kJ/mol

126
Q

How do elevators work?

A

Via the photoelectric effect

127
Q

Why does FADH2 transfer one electron to Fe-S at a time?

A

CoQ functions best when it takes 1 electron at a time

128
Q

What is the reduction potential equation?

A

ΔG = -nFΔEº

129
Q

What enzymes in the krebs cycle produce NADH?

A

α-ketoglutarate dehydrogenase complex
isocitrate dehydrogenase
malate dehydrogenase

130
Q

What are the direct products of glycolysis and what is the ATP yield from these?

A

2 NADH -> 3 or 5 ATP

2 ATP -> 2 ATP

131
Q

What are the direct products of pyruvate oxidation and what is the ATP yield from these?

A

2 NADH -> 5

132
Q

What are the direct products of acetyl CoA oxidation in Krebs cycle and what is the ATP yield from these?

A

6 NADH -> 15
2 FADH2 -> 3
2 ATP or GTP -> 2

133
Q

Why does the complete oxidation of glucose yield 30 or 32 ATP?

A

30 if we do not go through complex 1

134
Q

What happens when glycerol dehydrogenase phosphate 1 is high?

A

The body makes more fat because you have high sugar

135
Q

What basic reactions occur in the light reactions?

A

H2O to O2

NADP+ to NADPH

136
Q

What basic reactions occur in the dark reactions?

A

ADP + Pi to ATP

Carbohydrates to CO2

137
Q

Where do the light reactions occur?

A

Thylakoids

138
Q

Where do the dark reactions occur?

A

Stroma

139
Q

What are grana?

A

Stacks of thylakoid membranes

140
Q

What happens when light hits the leaves?

A

Light hits the antenna chlorophyll or carotenoids and it is absorbed and transferred between them until it reaches the reaction center

141
Q

What happens in the reaction center?

A

Photochemical reaction converts the energy of a photon into a separation of charge, initiating electron flow

142
Q

What residues are present in F0 of ATP synthase?

A

Asp

143
Q

Compare chlorophyll and hemoglobin

A

Structured the same except chlorophyll uses Mg2+ because Mg2+ has great light absorbing abilities

144
Q

What do X-Rays do to bonds?

A

Break them completely

145
Q

What do UV do to bonds?

A

Break most bonds

146
Q

What does IR do to bonds?

A

Vibrates the bonds which is how we get the IR spectrum

147
Q

What do microwaves do to bonds?

A

Causes the molecule to spin and hit surrounding molecules

148
Q

What are the most abundant in plants?

A

Chlorophyll A and B which will be destroyed fast so they’re the first to go and that’s why leaves turn orange and yellow

149
Q

What occurs in photosystem 2?

A

1) Light excites an antenna molecule which raises the electron to a higher energy level
2) Excited antenna passes electron to another antenna
3) Energy transferred to reaction center chlorophyll
4) Excited chlorophyll passes electron to electron acceptor
5) Electron hole in reaction center is filled by electron from electron donor

150
Q

How does an electron travel in PSII?

A

Pheo -> PQA -> PQB -> Cytbf6 complex -> plastocyananin -> PSI

151
Q

How does an electron travel through PSI?

A

e- gets excited -> A0 -> A1 -> Fe-S then iron sulfur protein transfers electron to NADP+ to make NADPH

152
Q

What activates ATP synthase in photosynthesis?

A

Proton gradient activates ATP Synthase

153
Q

What are the dark reactions also known as?

A

Carbon assimilation reactions

154
Q

Where does chlorophyll B have the highest absorbance?

A

450 nm

155
Q

Where does chlorophyll A have the highest absorbance?

A

At 410 nm and also high at 670 nm

156
Q

Where is the highest absorbance of beta carotene?

A

450 nm

157
Q

Where is the highest absorbance of phycocyanin?

A

620 nm

158
Q

Where is the highest absorbance of phycoerythrin?

A

580 nm

159
Q

What does PSI use?

A

Ferredoxin and plastocyanin

160
Q

What is used in CO2 reduction?

A

NADPH an ATP produced through light reactions

161
Q

What do CO2 reduction reactions induce?

A

The movement of protons from the stroma into the thylakoid and Mg2+ from the thylakoid to the stroma

162
Q

What conditions favor enzyme activity?

A

Alkaline conditions and high Mg2+ concentration

163
Q

What cycle is critical in seeds?

A

Glyoxylate cycle; produces succinate from acetyl CoA

164
Q

Why do plants also need to produce NADH?

A

For energy for catabolic processes

165
Q

What percentage of CO2 is in the body and outside? Compare to air

A

5% in the body, lower outside the body. CO2 more dense than air

166
Q

What protects from mosquitoes and how?

A

Mosquitoes smell CO2 and can sense the concentration and know to attack. Applying antiperspirant closes the pores so CO2 can’t come out

167
Q

What are the stages of the Calvin cycle?

A

1) Carbon fixation
2) Reduction
3) Regeneration of acceptor

168
Q

What is the enzyme responsible in plants for conversion of CO2 into an organic form and how present is it in plants?

A

RUBISCO

Makes up 50% of soluble proteins in plants because it has turnover rate of 3CO2/second

169
Q

When is rubisco inactive?

A

When ribulose 1,5-bisphosphate alone occupies its active site blocking a critical Lys residue.

170
Q

What do rubisco activase + ATP do?

A

Displace the ribulose-1,5-bisphosphate allowing the carbamoylation of the Lys residue by CO2. Mg2+ binds, polarizes and orients the reactants for nucleophilic attack on CO2 by a ribulose intermediate​

171
Q

What fixates Mg2+ in the calvin cycle?

A

Asp and Glu

172
Q

What amino acids do you need for the calvin cycle to proceed?

A

Lys, Arg, Glu, and His

173
Q

What is the intermediate formed from ribulose-1,5-bisphosphate?

A

Enediolate by reacting with His and His extracts a proton

174
Q

What does a transketolase do?

A

Uses TPP prosthetic group and Mg2+ and moves 2 carbon ketol group to an aldose acceptor

175
Q

What does the synthesis of large carbohydrates start with?What is it converted into?

A

Glyceraldehyde-3-PO4

Starch for storage and sucrose for transport

176
Q

Where is sucrose made? Starch?

A

Cytosol

Stroma

177
Q

What does the pi-triose phosphate antiporter do and how?

A

Facilitates movement of ATP and electrons from stroma to cytosol
As dihydroxyacetone PO4 moves from stroma to cytosol, Pi moves in opposite.
As 3-phosphoglycerate moves form stroma to cytosol, Pi moves other way

178
Q

What is UDP and what does it do?

A

Activated form of glucose most often used in carbohydrate synthesis and cellulose synthesis
Sucrose produced from it

179
Q

Where does the glucose needed for the synthesis of cellulose come from?

A

Derives from sucrose, the normal transport system for glucose in plants​

180
Q

What does sucrose synthase do?

A

Generates UDP glucose after it is bound to sitosterol

181
Q

What does fatty acid biosynthesis require?

A

Acetate which is shuttled out of the mitochondria as citrate

182
Q

What is the main fatty acid we produce?

A

Palmitic acid

183
Q

What occurs in the cytosol in animal cells?

A

NADPH production
Isoprenoid and sterol synthesis (early stages)
Fatty acid synthesis

184
Q

What occurs in the ER in animal cells?

A

Phospholipid synthesis
Sterol synthesis (late stages)
Fatty acid elongation
Fatty acid desaturation

185
Q

What occurs in the mitochondria in animal cells?

A

Fatty acid oxidation
Acetyl CoA production
Ketone body synthesis
Fatty acid elongation

186
Q

What occurs in the mitochondria of animal cells?

A

No fatty acid oxidation

187
Q

What occurs in the chloroplasts of plant cells?

A

NADPH and ATP Production

Fatty acid synthesis

188
Q

What occurs in the peroxisomes of plant cells?

A

Fatty acid oxidation

Catalase, peroxidase

189
Q

What does the biosynthesis of fatty acids require and what is it made by?

A

Requires malonyl-CoA which is made by 3 functional regions of acetyl CoA carboxylase

1) Biotin Carboxylase
2) Biotin Carrier Protein
3) Transcarboxylase

190
Q

What does Malonyl-CoA do in fatty acid synthase and how?

A

Adds 2 carbons in a 4 step sequence. First 2 steps introduce acetyl group and remove CO2. Second 2dehydrate and convert initial acetyl to a saturated ethyl group.

1) Condensation (removes CO2)
2) Reduction (NADPH->NADP+)
3) Dehydration (Removes Water)
4) Reduction (NADPH-> NADP+)

191
Q

What is the precursor of other long chain fatty acids?

A

Palmitate

192
Q

What can’t mammals do?

A

Convert oleate to linoleate

193
Q

What is desaturation performed by?

A

A mixed-function oxidase using NADPH and O2 as electron acceptor

194
Q

What does desaturation of palmitate 16:0 produce?

A

Palmitoleate 16:1 (Δ9)

195
Q

What does elongation of palmitate produce?

A

Stearate 18:0

196
Q

What does elongation of stearate 18:0 produce?

A

Longer saturated fatty acids

197
Q

What does desaturation of stearate 18:0 produce?

A

Oleate 18:1 (Δ9)

198
Q

What does desaturation of oleate 18:1 (Δ9) produce?

A

Linoleate 18:2 (Δ9,12)

199
Q

What does desaturation of Linoleate 18:2 (Δ9,12) produce?

A

α-linolenate 18:3 (Δ9,12,15)

γ-linolenate 18:3 (Δ6,9,12)

200
Q

What does elongation of γ-linolenate 18:3 (Δ6,9,12) produce?

A

Eicosatrienoate 20:3 (Δ8,11,14)

201
Q

What does saturation of Eicosatrienoate 20:3 (Δ8,11,14) produce?

A

Arachidonate 20:4 (Δ5,8,11,14)

202
Q

Where does destauration take place and what does it use?

A

In the smooth ER and uses mixed-function oxidases

203
Q

What are oxidases?

A

Use O2 as electron acceptor but O2 is not incorporated in the molecyle

204
Q

What are oxygenases?

A

Use O2 and incorporate one O (monooxygenases) or 2 (disoxygenases) in the molecule

205
Q

what are the two main routes for NADPH production?

A

Malic Enzyme

Pentose Phosphate Pathway

206
Q

What are eicosanoids formed from and where is what they’re formed from stored?

A

Arachidonate

Stored in middle carbon of glycerol in membrane phospholipids

207
Q

What does cyclooxygenase COX do?

A

Comes from smooth ER and converts arachidonate to prostaglandin H2, precursor of other prostaglandins and thromboxanes

208
Q

What type of addition does COX perform?

A

3+2

209
Q

How does COX affect inflammation?

A

Aspirin and Ibuprofen block COX which reduced inflammation

210
Q

What type of hormones are Eicosanoids?

A

Paracrine

211
Q

What does leukotriene synthesis use?

A

Lipooxygenases found in leukocytes, heart, brain, lung, and spleen

212
Q

To what family do lipoxygenases belong?

A

P-450 family, not inhibited by NSAIDs

213
Q

What are TAGs and glycerophospholipids made from?

A

Fatty acyl CoA

L-glycerol-3-PO4 (derived mostly from glycolysis

214
Q

What does L-glycerol 3-

PO4 make and how?

A

Phosphatidic acid via 2 acyl transferases which can be converted to TAGs or glycerophospholipids

215
Q

What does glyceroneogenesis use?

A

Glycerol 3 PO4 made by adipose tissue and has a link to type 2 diabetes, and controls the rate of fatty acids released in the blood

216
Q

What does glyceroneogenesis account for during fasting?

A

65% of fatty acids reesterified to TAGs

217
Q

Synthesis of cholesterol?

A

1) Condensation of 3 acetate units make mevalonate
2) Mevalonate is converted to activated 5-carbon isoprene
3) Six units of isporene polymerize to form squalene (from sharks)
4) Cyclization of squalene to form, after some oxidation and methyl shifts, the 4 rings of cholesterol

218
Q

What is cholesterol converted to?

A

Hormones, bile acids, or hydrophobic esters for storage and transport as lipoproteins

219
Q

Describe trends going from Chlyomicron to VLDL to IDL to LDL to HDL?

A

Protein increases
TAGs decreases
Cholesterol Esters increase
Phospholipids increase

220
Q

How do we transport fats?

A

Through lipoproteins

221
Q

What is lipoprotein lipase?

A

A member of the serine esterase family (like trypsin) with active site Ser, His, and Asp

222
Q

What does the liver orchestrate?

A

Lipoprotein transport pathways to redistribute fat and cholesterol

223
Q

How do fats enter the liver?

A

Fats -> Chylomicron -> remnants of chylomicron and cholesterol go into liver and leave as VLDL

VLDL goes through capillaries and remnants produced are IDL which can go into liver or get converted to LDL which enters the liver

LDL has receptor and can make HDL which can go to liver or to produce steroids

224
Q

What is atmospheric N2 fixed by?

A

Some bacteria and archaea in the nitrogenase complex

225
Q

Where does NH4+ in plants come from?

A

NO3- reduced to NO3- reductase and NO2 reductase

226
Q

What is NH4+ in plants converted to?

A

Glutamine by reaction with glutamate catalyzed by glutamine synthetase then glutamine is converted to glutamate by glutamate synthase

227
Q

Where are all aminoacids derived from?

A

Intermediated of glycolysis, citric acid cycle, or pentose phosphate pathway

228
Q

How does nitrogen enter various pathways?

A

By glutamate and glutamine

229
Q

Where does ribose-5-PO4 make?

A

Histidine

230
Q

Where does serine come from and what does it make?

A

3-phosphoglycerate and it makes glycine and cysteine

231
Q

What aa does phosphoenolpyruvate make?

A

Tryptophan
Phenylalanine
Tyrosine

232
Q

What aa does pyruvate make?

A

Alanine
Valine
Leucine
Isoleucine

233
Q

What aa does oxaloacetate make?

A

Aspartate which makes asparagine, methionine, threonine, and lysine

234
Q

What aa does alpha ketoglutarate make?

A

Glutamate which makes glutamine, proline, and arginine

235
Q

What are the essential aa?

A 
Val
Ile
Leu
Met
Thr
Lys
His
Phe
Trp
236
Q

What is phosphocreatine made by?

A

Glycine
Arginine
Methionine

237
Q

What composes glutathione

A

γ-Glu-Cys-Gly via the usage of 2 ATP and the use of γ-glutamyl cysteine synthetase and glythathione synthetase

238
Q

What are derivatives of tyrosine?

A

Epinephrine, norepinephrine, and Dopamine. Norepinephrine involves Vit C

239
Q

What is produced from glutamate?

A

GABA and it involves removal CO2

240
Q

What is produced from histadine?

A

Histamine and it involves removal of CO2

241
Q

Where does seratonin come from?

A

Tryptophan

242
Q

How is nitric oxide made?

A

From arginine via NADPH+O2 and a hydroxyarginine intermediate that will react to form citrulline and NO

243
Q

How does DNA get converted to a polypeptide?

A

DNA (double strand) to mRNA (single strand) to polypeptide

244
Q

What is the function of the centromere?

A

A link to the mitotic spindle

245
Q

What are telomeres?

A

Repeated sequences that help stabilize the chromosome

246
Q

How is cellular DNA compact and compare it to the cellular environment?

A

It is compact by supercoiling but still is underwound in the cellular environment

247
Q

What does underwiring promote?

A

Cruciform formation and topoisomerases catalyze the extent of underwinding

248
Q

What do Topo I and II do?

A

I breaks one strand (Lk=1)

II breaks both both strands (Lk=2)

249
Q

Steps of topoisomerase

A

1) Active Site Tyr attacks phosphodiester bond in one DNA strand and creates covalent linkage
2) Enzyme changes to open conformation
3) Unbroken DNA strand passes through break in the first strand
4) Enzyme in closed conformation; liberated OH attacks protein linkage to religate the strand

250
Q

What does chromatin contain?

A

Basic histone proteins that have 1/4 Arg and Lys residues

251
Q

What does packagine of the final chromosome start with?

A

Nucleosome

252
Q

What is DNA replication and where does it start and proceed?

A

Semiconservative, semidiscontinuous

Starts at an origin and proceeds 5’->3’

253
Q

What is DNa made by and degraded by?

A

Made by DNA polymerase

Degraded by nucleases

254
Q

What are endo and exonucleases?

A

Exonuxleases degrade at ends

Endonucleases at internal sites reducing it to smaller and smaller fragments

255
Q

What does DNA polymerase contain?

A

2 Asp

2 Mg2+

256
Q

What serves as a template and primer strand and what does it provide?

A

Single unpaired strand

Provides the free 3’OH to which the new nucleotide is added. Migration occurs after to make room for next addition

257
Q

What are many primers?

A

Oligonucleotides of RNA made by dedicated enzymes when needed. The number of nucleotides added before polymerase dissociations is processivity

258
Q

Comparison of DNA polymerases

A

I, II, & III all move 3’ to 5’
Only I moves 5’ to 3’
III does the synthesis of DNA
Processivity increases from I to II to III

259
Q

What happens if an addition error occurs?

A

Translocon is inhibited. A 3’-> 5’ exonuclease removed the mispaired nucleoride and the polymerase begins again

260
Q

What are the components of the replisome?

A

Primosome and 2 poly III for each strand

Primosome has primase, helicase, and accessory proteins

261
Q

Role of Helicase

A

Unwinds double helix

262
Q

Role of primase

A

Synthesizes RNA primers

263
Q

Role of Single-strand binding proteins

A

Stabilizes single stranded regions

264
Q

Role of DNA gyrase

A

Relives torque

265
Q

Role of DNA polymerase III

A

Synthesizes DNA

266
Q

Role of DNA polymerase I

A

Erases primer and fills gaps

267
Q

Role of DNA ligase

A

Joins the ends of DNA segments; DNA repair

268
Q

What must happen to chromatin?

A

Must be dismantled prior to the replication fork in eukaryotic replication

269
Q

How does helicase unwind the material?

A

Uses ATP

270
Q

What is Topoisomerase I attached to?

A

Tyrosine

271
Q

Function of mRNA

A

Encodes aa specified by a gene or set of genes

272
Q

Function of rRNA

A

Part of ribsomes, the makers of proteins

273
Q

Function of tRNA

A

Reads mRNA and transfers the given aa to a polypeptide chain

274
Q

Lagging strand synthesis

A

Primers made by primase are removed by Poly I via its 5’->3’ exonuclease. Nick between fragments is sealed by DNA ligase

275
Q

What is the synthesis of RNA done by?

A

A DNA dependent RNA polymerase in a way chemically equivalent to DNA replication

276
Q

Why does RNA not require primer or proof reading?

A

DNA is more important

277
Q

Where does RNA synthesis begin?

A

Specific DNA sequences called promoters. The RNA transcript is identical to the nontemplate strand but T is replaced by U

278
Q

Where are most RNAs made and what do they serve?

A

They are outside classical mRNAs tRNAs and rRNAs. They serve special functions such as regulation. Syntehsis in 5’ to 3’

279
Q

What is the initial RNA made?

A

Primary transcript and contains introns which are spliced to join the exons into a unit that specifies a functional polypeptide

280
Q

How can a gene give rise to multiple products?

A

Differential processing generating two isozymes, for example

281
Q

What does the cdentral dogma include?

A

RNA dependent synthesis of DNA y reverse transcriptases and RNA. RNA viruses provide the most characterized RNA polymerases

282
Q

DNA replication

A

DNA template directed duplication of he genome prior to cell division

283
Q

Transcription

A

DNA template-directed biosynthesis of RNA

284
Q

Reverse Transcription

A

RNA template-directed biosynthesis of DNA

285
Q

Translation

A

mRNA template-directed biosynthesis of proteins

286
Q

Where does synthesis of proteins take place?

A

In the ribosomes that are attached externally to the ER ​

287
Q

What does the anticodon loop contain?

A

A trinucleotide sequence called the anticodon that is complementary to the appropriate trinucleotide codon in the mRNA.​

288
Q

What are the stop codons

A

UAA
UAG
UGA

Bio 3100 (6 decks)

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