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Biochemistry 1 > Test 2 > Flashcards

Test 2 Flashcards

1
Q

What are proteins made of?

A

Amino acids

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2
Q

What are carbohydrates?

A

Sugars molecules (monosaccharides, polysaccharides, glucose)

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3
Q

What are lipids made out of?

A

Fatty acids and a glycerol

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4
Q

What are DNA and RNA?

A

They are nucleic acids

DNA - deoxyribonucleic acid

RNA - ribonucleic acid

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5
Q

Enzyme structure

A

Enzymes are proteins, they have a globular shape.

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6
Q

What is a prosthetic group?

A

a metal or other co-enzyme covalently bound to an enzyme

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7
Q

What is a holoenzyme?

A

a complete, catalytically active enzyme including all co-factors

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8
Q

What is and apoenzyme?

A

The protein portion of a holoenzyme minus the co-factors

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9
Q

What is an Isozyme?

A

an enzyme that performs the same or similar function to another enzyme.

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10
Q

What are enzymes known for being?

A

Catalysts - they greatly increase the rate of spontaneous reactions

(Catalytic power 10^6 - 10^12)

For reversible reactions, they speed progress to equilibrium

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11
Q

Can enzymes increase the rate of reactions without increasing the temperature? If so how?

A

Yes they can, they do this by lowering the activation energy.

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12
Q

Cycle of enzymes

A

Substrate connects to active site

Products are released

Enzyme is released unchanged

Cycle repeats

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13
Q

The lock and key hypothesis vs the induced fit hypothesis

A

The lock and key hypothesis:
The substrate and active site fit with each other like a lock and key. Then the products form in a different shape from the substrate and get released.

The induced fit hypothesis:
When the substrate combines with an enzyme, it induces a change in the enzyme’s conformation (shape). The active site is then molded into a precise conformation.

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14
Q

Factors that affect enzymes

A

Temperature
pH
substrate/enzyme concentration
cofactors and coenzymes
inhibitors

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15
Q

The effect of temperature on enzymes

A

When the temperature is too high the proteins will denature

To avoid this we need to keep a balance between Q10 and denaturation

Q10 - the increase in reaction rate with a 10*C rise in temperature

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16
Q

What is the optimum temperature for most enzymes?

A

about 30*C

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17
Q

The effect of pH on enzymes

A

Extreme pH levels will produce denaturation
- the structure of the enzyme is changed
- The active site is distorted and the substrate molecules will no longer fit in it

At slightly changed pH values from the enzymes optimum pH, small changes will occur to the enzymes charge and substrate molecule

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18
Q

the effect of Substrate/Enzyme concentration on enzymes

A
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19
Q

What are enzyme cofactors? and what is the difference between cofactors and coenzymes?

A

Enzyme cofactors - Inorganic ions or organic non-protein groups necessary for catalysis to occur

Cofactors - metallic ions

Coenzymes - organic cofactors such as vitamins

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20
Q

What are inhibitors? What are the different types?

A

Inhibitors - chemicals that reduce the rate of enzymatic reactions (block enzymes)

There are two different types
- Irreversible inhibitors
- Reversible inhibitors

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21
Q

Mechaelis-Menten kinetics

A

Kinetics that are used too measure how fast an enzyme works.

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22
Q

Lineweaver-Burke plot

A

Differs a little from the Mechaelis-Menten kinetics plot in that its usually straight.

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23
Q

Reversible inhibitors divide into:

A

If inhibitors are present:
- competitive inhibitors are molecules that bind to the same site as the substrate -
preventing the substrate from binding as they do so - but are not changed by the enzyme.

  • noncompetitive inhibitors bind to some other site on the enzyme reducing its catalytic
    power
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24
Q

What is the “turnover number” ?

A

the overall synthesis and degradation of a particular enzyme.

It’s one way to regulate the quantity of an enzyme

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25
Q

What are zymogens?

A

inactive precursor proteins

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26
Q

Enzyme/substrate compartmentation

A

Segregation of metabolic processes into distinct subcellular locations like the specialized organelles (nucleus, endoplasmic reticulum, golgi aparatus, lysosomes, mitochondria, etc.) is another form of regulation.

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27
Q

With what does allosteric regulation occur? And what is high-affinity and low-affinity state?

A

Allosteric regulation occurs with reversible combinations of regulatory molecules with an allosteric site on the enzyme

High-affinity state (active form) - enzyme binds substrate strongly

Low-affinity state (inactive form) - enzyme binds substrate weakly or not at all

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28
Q

Allosteric activators vs allosteric inhibitors

A
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29
Q

What are hemoglobin and myoglobin?

A

oxygen transport and storage proteins

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30
Q

Hemoglobin and myoglobin structures

A
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31
Q

Positive cooperativity (Hb)

A

when deoxyhemoglobin binds a single oxygen, it causes the other heme groups to become much more likely to bind other oxygen molecules

(this is what we call positive cooperativity)

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32
Q

3 important factors in hemoglobins binding of oxygen

A

Hb must be able to bind oxygen in the lungs

Hb must be able to release oxygen in capillaries

If Hb behaved like Mb, very little oxygen would be released in capillaries

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33
Q

Explain the Bohr Effect part 1 and mention who it was discovered by.

A

It was discovered by Christian Bohr

Its competition between oxygen and H+

It has important physiological significance

Binding of protons diminishes oxygen binding

Binding of oxygen diminishes proton binding

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34
Q

Explain the Bohr Effect part 2

A

In this part carbon dioxide diminishes oxygen binding

Hydration of CO2 in tissues and extremities leads to proton production

These protons are taken up by Hb as oxygen dissociates

The reverse occurs in the lungs

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35
Q

2,3-Bisphosphoglycerate and its effect on hemoglobin

A

An allosteric effector of hemoglobin

In the absence of 2,3-BPG, oxygen binding to Hb follows a rectangular hyperbola!

The sigmoid binding curve is only observed in its presence

Since 2,3-BPG binds at a site distant from the Fe where oxygen binds, it is called an allosteric effector

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36
Q

Covalent modification properties

A

Regulation by covalent modifications is slower than by allosteric regulation.

It’s reversible

Requires one enzyme for activation and one enzyme for inactivation

It freezes enzyme T or R conformation

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37
Q

Phosphorylation/Dephosphorylation properties

A

Most common covalent modification

Involves protein kinases/phosphatase

PDK inactivated by phosphorylation

Amino acids with -OH groups are targets for phosphorylation

Phosphates are bulky (-) charged groups which effect conformation

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38
Q

Enzymes as diagnostic indicators

A

The activities of many enzymes are routinely determined in plasma for diagnostic purposes in diseases of the heart, liver, skeletal muscle, pancreas and other tissues

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39
Q

One international unit vs Katal

A

One international unit (IU) is the amount of enzyme that will convert one micromole of substrate per minute per liter of sample. It is written as U/L.

Katal (Catalytic activity) is defined as the number of mole of substrate transformed per second per second per liter of sample

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40
Q

Enzymes in clinical diagnosis secretory vs intracellular

A

Secretory - produced by tissues (namely liver), acting in plasma.

Intracellular - function intracellular, have no physiological use in plasma

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41
Q

Where is Alkaline phosphate (ALP) present and what are its normal levels?

A

Its normal serum level is 40-120 U/L or 0.5 - 1.3 mmol/(hour*L)

This enzyme is present in high concentrations in the liver, bone, placenta and intestinal epithelium

42
Q

Usual causes for an increase in plasma ALP activity

A

Pathological (often >5 xULN)
- paget’s disease or bone osteomalacia
- rickets
- cholestasis (intra- and extrahepatic)
- cirrhosis

Usually <5 xULN
- bone tumors (primary and secondary)
- primary hyperparathyroidism with bone involvement
- healing fractures
- osteomyelitis
- hepatic space-occupying lesions (tumor, abscess)

43
Q

Acid phosphate (ACP) normal value, and other important factors.

A

Normal serum value 2.5 - 12 U/L or 0.025 - 0.12 mmol/(hour*L)

It’s value is increased in prostate cancer and highly elevated in bone metastasis of prostate cancer

It’s therefore an important tumor marker

It’s present in high concentrations in semen. This is used in rape investigations.

44
Q

What are the two aminotransferases used in diagnosis and management and what are their normal levels?

A

Aspartate aminotransferase (AST) also known as Serum Glutamate-Oxoloacetate Transaminase (SGOT)

It’s normal level is 8 - 40 U/L or 0.1 - 0.45 mmol/(hour*L)

and

Alanine aminotransferase (ALT) also known as Serum Glutamate-Pyruvate Transaminase (SGPT)

It’s normal level is 5 - 30 U/L or 0.1 - 0.68 mmol/(hour*L)

45
Q

Which enzymes are increased in liver disease?

A

ALT and AST, but ALT > AST

46
Q

Lactate dehydrogenase (LDH) (LD) normal value.

A

It’s normal value is 100 - 200 U/L

47
Q

Creatinine kinase (CK) normal value.

A

Normal value 15 - 100 U/L for males and 10 - 80 U/L for females

48
Q

Causes for CK increase

A

> 10 xULN
- Polymyositis
- rhabdomyolysis
- duchenne muscular dystrophy
- myocardial infarction

5-10 xULN
- following surgery
- skeletal muscle trauma
- severe excersize
- myositis
- carriers of Duchenne muscular dystrophy

<5 xULN
- physiological ( afro-caribbeans)
- hypothyrodism
- drug (statin) treatment

49
Q

Gamma glutamyl transferase (GGT) normal value, where is it normally found and when is it normally increased?

A

Normal value is 6 - 45 U/L in male and 5 - 30 U/L in female

Its value is moderately increased in infective hepatitis and prostate cancers. It’s highly elevated in alcoholism, obstructive jaundice and neoplasm’s of liver

50
Q

Amylase normal value, where is it produced and when is its value increased.

A

It’s normal value is 50 - 120 U/L ( 12- 32 g/(hour*L))

It is produced by the pancreas and salivary glands

its value is increased in acute and chronic pancreatitis. Also in mumps, obstruction of pancreatic duct and in renal disease.

51
Q

Prostate specific antigen (PSA) normal value, where it is produced, values of benign prostate enlargement and of prostate cancer

A

normal value 1 - 5 µg/L

It is produced in the secretory epithelium of prostal gland

In the case of benign prostate enlargement the value is 4 - 10 µg/L

and for prostate cancer it is 10 µg/L

52
Q

What is bioenergetics?

A

A discipline within biochemistry dedicated to the study of energy flow within living systems

53
Q

Energy, potential vs kinetic

A

Energy - capacity to perform work

Potential - energy of position, chemical bonds, water behind a dam

Kinetic - energy of motion, heat, light energy

54
Q

The first and second law of thermodynamics

A

First - energy cannot be created or destroyed, but only converted into other forms
-> amount of energy in the universe is constant

Second - all energy transformations are inefficient because every spontaneous reaction results in an increase in entropy and the loss of usable energy as heat
-> increasing the entropy and loose usable energy as heat

55
Q

Why is energy transformation needed in living organisms?

A

(1) the performance of mechanical work in muscle contraction and cellular movements

(2) the active transport of molecules and ions

(3) the synthesis of macromolecules and other biomolecules from
simple precursors

56
Q

Two types of metabolism

A

Catabolism - The conversion of energy from fuels into biologically useful forms

Fuel (carbohydrates, fats) = CO2 + H2O + useful energy

Anabolism - Reactions that require inputs of energy to proceed

Useful energy + simple precursors = complex molecules

57
Q

Gibbs free energy

A

Change in free energy (ΔG) = a portion of a total energy that is useful for doing work

ΔG<0 = reaction proceeds spontaneously with loss of free energy

ΔG>0 = the reaction proceeds only if free energy can be gained

58
Q

How do we recognise increased entropy in reactions?

A

if there are more products than reactants, we have increased entropy.

59
Q

How does coupling affect thermodynamically unfavourable reactions?

A

They can be coupled to a favourable (exergonic) reaction, given they have a common intermediate, so that the exergonic reaction drives the endergonic. this is what ATP is used for

60
Q

ATP hydrolysis reaction coupled with endergonic condensations

A

ATP is used to transfer highly energetic Po3 to the substrate, turning it into a high energy compound that will easily react with the other reactant.

61
Q

ATP Hydrolysis

A

ATP is hydrolysed by H20, breaking the high energy phosphoanhydride bonds and creating ADP or if done further, even AMP, releasing more energy.

62
Q

What can explain the high phosphoryl-transfer potential of ATP?

A

features of the ATP structure:

1) Resonance stabilisation

  • Pi is more stable than ATP

2) Electrostatic repulsion

  • four negative charges in ATP repel one another, more than in ADP

3) Increase in entropy

  • entropy of the ATP hydrolysis is greater

(more products)

4) stabilisation due to hydration

Water binds to ADP and Pi, stabilising them. (more stable than ATP, carrying less energy)

63
Q

Phosphoryl-transfer potential

A

The standard free energy of hydrolysis.
-comparing the tendency of organic molecules to transfer a phosphoryl group to an acceptor molecule.

64
Q

ATPs phosphoryl-transfer potential

A

is intermediate, among the other phosphorylated molecules.

65
Q

three molecules with higher phosphoryl-transfer potential than ATP

A

Phospoenolpyruvate
1,3-Biphosphoglycerate
Creatine phosphate

66
Q

Whats the most important property of phosphate esters?

A

they are thermodynamically unstable while being kinetically stable, meaning that they are resistant to hydrolysis in absence of enzymes
-They are ideal regulatory molecules added to proteins by kinases and removed by phosphatases.

67
Q

Creatine phosphate

A

An energy storage molecule used by muscle tissue. The phosphate from creatine phosphate can be removed and attached to an ADP to generate ATP quickly. it is reversible and if the ATP levels are high after work, the creatinekinase transfers phosphate back to creatine phosphate and stores it in the muscle.

68
Q

ATP-ADP cycle

A

Process by which cells regenerate ATP. ADP forms when a phosphate group is removed from ATP, then ATP forms again as ADP gains a phosphate group.
-fundamental mode of energy exchange in biological systems.

69
Q

Sources of ATP

A
  1. Oxidative phosphorylation; major source
  2. Substrate level phosphorylation

3.Kinases

70
Q

Oxidative phosphorylation

A

The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.- generates a lot of energy and is therefore broken down into smaller steps.

71
Q

substrate-level phosphorylation

A

Directly phosphorylating ADP with a phosphate and energy provided from a coupled reaction.
- compounds with a high phosphoryl-transfer potential can couple CO2 to ATP synthesis.

This is used in Krebs cycle and glycolysis

72
Q

Difference between oxidative phosphorylation and substrate level phosphorylation

A

Oxidative phosphorylation =uses proton gradient to make it happen

Substrate level = more direct transfer

73
Q

Adenylate kinase

A

Enzyme that catalyzes reaction 2ADP -> ATP + AMP when ADP levels increase in working muscle.
(AMP signals for glucose and fatty acid oxidation -> increase metabolism) ATP

74
Q

ATP hydrolysis to AMP

A

Releases PPi, which can be hydrolysed by an inorganic phosphatase, releasing energy and driving reaction to the right - generating heat.

-> this hydrolysis of ATP to AMP is required to activate long chain fatty acids

75
Q

Synthetases and synthases

A

Synthetases require ATP
Synthases do not

76
Q

Explain the phosphorylation of nucleoside monophosphate (NMP) and diphosphates (NDP)

A

NMP can be phosphorylated by ATP into NDP or even further into Nucleoside triphosphate (NTP).

NTPs make DNA but also Activate molecules like glucose
- Glu-UDP must be activated to form Glu-UTP

77
Q

Redox potential

A

tendency of reactants to donate/accept electrons.

78
Q

high redox potential

A

Will get oxidised (donate e-) - strong reductant

79
Q

Oxidases

A

Uses oxygen as hydrogen/electron acceptor

80
Q

Cytochrome oxidase

A

An enzyme with two ´heme prosthetic groups “a” and “a3” Each have Fe atom fluctuating between Fe2+ and Fe3+.

  • this is the terminal component of the electron transport chain in mitochondria, where it transfers electrons from the oxidation of substrates, to oxygen.
81
Q

Flavoproteins

A

contains flavin prosthetic group (e.g., FMN, FAD) that accepts 2 electrons and 2 protons.

L-amino acid oxidase

-enzyme that does oxidative deamination of amino acids

xanthine oxidase

-converts purin into uric acid

Aldehyde dehydrogenase

-an enzyme that oxidizes acetaldehyde to acetate in alcohol detoxification.

82
Q

dehydrogenases

A

cannot use oxygen as hydrogen acceptor. they use NAD+ and NADP+ or they depend on riboflavin (FMN, FAD)

  • they transfer hydrogen from one substrate to another
  • they transfer electrons in the electron transport chain.
83
Q

Activated carriers

A

molecules used to carry electrons generated during glycolysis.

  • FAD
    -NAD+
    -NADP+
84
Q

flavin adenine dinucleotide (FAD)

A

coenzyme that shuttles protons and electrons from glycolysis and the Krebs cycle to the electron transport chain.
- Its oxidised form is FAD and reduced is FADH2.

85
Q

FAD in Krebs Cycle

A

oxidises succinate to fumarate, by accepting two hydrogens and become FADH2.

86
Q

nicotinamide adenine dinucleotide (NAD+)

A

Has a nicotinamide ring which accepts H+ + 2e- and becomes NADH and thereby oxidises its substrate.
- it is used in glycolysis.

87
Q

Describe the cell ratios of NAD+/NADH and NADP+/NADPH

A

of NAD+/NADH, there is 1000 x more NAD+ (oxidised form) inside the cell, because its ready to perform dehydrogenations

of NADP+/NADPH, there is 100 x more NADPH (reduced form) inside cell, to provide reducing power for synthesis of cholesterol, steroid hormones fatty acids etc.

88
Q

Whats the difference between NAD+ and NADP+

A

NAD+ is used in catabolism

NADP+ is used in anabolism

-the phosphate group on C2 of ribose on NADP+ has an enormous consequence; it is used as a tag for enzymes to recognise and distinguish between electrons to be used in anabolism or catabolism.

89
Q

NADPH is used as

A

A reducing power in most reductive biosyntheses. it gives away H+ and becomes oxidised, to reduce its substrate.

90
Q

Hydroperoxidases (peroxidase and catalase)

A

Protects the body against harmful effects of reactive oxygen species. it uses various electron acceptors.

-An example of such an enzyme is; Glutathione peroxidase in eyrthrocytes

91
Q

glutathione peroxidase

A

Protects membrane lipids and haemoglobin from reactive oxygen species. it uses a reduced glutathione and converts it into oxidised form

H2O2 + reduced glutathione –> 2 H2O + Oxidised glutathione

92
Q

Oxygenases

A

oxidize the substrate molecule using oxygen.

(Substrate) A + O2 –> AO2

93
Q

stages of catabolism

A

1) In cytosol:
-Large molecules in food are broken down into smaller units in digestion

2) Inner mitochondrial membrane:
-Small molecules are then degraded to simpler units (acetyl coA) playing a central role in metabolism

3) mitochondrial matrix:
- ATP is produced from the complete oxidation of the acetyl unit of acetyl coA, through citric acid cycle and oxidative phoshorylation

94
Q

Components of the electron transport chain

A

Multiprotein complexes:

Complex 1,3,4 - span the membrane and are PUMPS.

Complex 2 is smaller, doesn’t span the membrane

Electroncarriers:

Coenzyme Q

Cytochrome C

  • electrons flow from high energy complex 1 to lower energy complex 4-. this flow is highly exergonic and generates a force, transporting protons across the membrane.
95
Q

Iron-sulfur clusters

A

Electroncarriers present inside the protein complexes (1,2,3) of the electron transport chain.

  • they have fluctuating Fe2+/Fe3+ ions that will transport these electrons.
96
Q

Cytochrome C

A

A coenzyme/electron carrier in the electron transport chain. it is very evolutionary conserved and is similar in all species.

97
Q

Q-cycle

A

Is a part of complex II function, since coenzyme Q coming with the electrons carries 2, while CytC can only carry 1 e-.
The Q-cycle is used to store the extra electron before transporting it.

98
Q

ATP synthase

A

Large protein in the mitochondrial membrane, that transports H+ back to the matrix after being pumped through electron transport chain. it uses the energy from these H+ to bind ADP and a phosphate group together to produce ATP

it has a two units;
F0 is the channel/proton-conducting unit
F1 is the catalytic/synthetic unit

  • 3H+ flow = 1 ATP
99
Q

Give the basic overview of oxidative phosphorylation

A

1) ETC generate a H+ gradient -> force

2) H+ come back to the matrix by ATP synthase
- they flow through F0 channel and cause movement of F1 unit -> condensation of ADP + PO3 -> ATP.

100
Q

How can ATP Synthase be regulated?

A

1) The mitochondria contain an evolutionary conserved protein, Inhibitory factor 1 (F1).

  • it specifically inhibits the potential hydrolytic activity of the synthase, preventing wasteful hydrolysis of ATP.

2) The uncoupling protein UCP-1 (thermogenin) is physiologically present in brown adipose tissue. it allows protons to flow through without ATP synthase -> generates heat.

Biochemistry 1 (19 decks)

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