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Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Which type of chemical bonds are strongest?

A

Covalent bonds

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2
Q

Electronegativity is…

A

The attractive force that an atomic nucleus exerts on electrons

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3
Q

Electronegativity of carbon is greater than the electronegativity of hydrogen. Which is reduced?

A

Carbon has a greater attractive force for electrons, so it gains electrons, therefore it is reduced and hydrogen is oxidised

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4
Q

Reducing agents are themselves oxidised. True/False?

A

True

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5
Q

First law of thermodynamics?

A

Energy is neither created or destroyed

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6
Q

Second law of thermodynamics?

A

When energy is converted to another form, some of it is lost (never 100% efficient)

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7
Q

∆G = the change in free energy = ?

A

∆H - T∆S

∆G°’ + RTln([C][D]/[A][B])

Energy in products - Energy in reactants

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8
Q

Exergonic reactions are where…

A

Products have less free energy than the reactants
∆G is -ve
Reaction can occur spontaneously

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9
Q

Endergonic reactions are where…

A

Products have greater free energy than the reactants
∆G is +ve
Reaction cannot occur spontaneously

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10
Q

The difference between normal standard conditions and biochemical standard conditions is…

A

pH = 7, T = 298K

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11
Q

At equilibrium ∆G = 0. This is characteristic of readily reversible reactions. True/False?

A

True

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12
Q

Reaction spontaneity can be achieved by…

A

Changing concentration of reactants/products
Coupling with highly favourable processes (e.g. with hydrolysis of ATP)
Both of the above help ∆G become -ve

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13
Q

Amino acids are subdivided into 4 groups, which are?

A

Non-polar hydrophobic
Polar uncharged
Acidic (-COOH)
Basic (-NH)

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14
Q

The N-terminal of a peptide chain is -ve. True/False?

A

False

It is +ve due to NH3

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15
Q

The C-terminal of a peptide chain is -ve. True/False?

A

True due to COO-

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16
Q

A zwitterion has which type of charge?

A

None! No net charge

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17
Q

Ka = acid dissociation constant = ?

A

[H+][A-]/[HA]

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18
Q

pH = measurement of how many H+ in a solution = ?

A

-log10[H+]

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19
Q

Henderson Hasselbach Equation connects Ka of a weak acid with the pH of a solution containing this acid. The equation is…

A

pH = pKa + log[A-]/[HA]

pKa - pH = log[HA]/[A-]

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20
Q

Primary protein structure describes…

A

The specific sequence of amino acids in a chain

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21
Q

Secondary protein structure describes…

A

The hydrogen-bonded 3D arrangement of the chain
α-helix (one peptide chain spiralled; right-handed)
B-stranded-sheet or B-pleated-sheet

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22
Q

Tertiary protein structure describes…

A

The arrangement of the chain in space and forces stabilising the structure

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23
Q

Quaternary protein structure describes…

A

Association of non-protein groups to the chain

e.g. haemoglobin, myoglobin

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24
Q

What is the central dogma?

A

DNA is transcribed to RNA, which is translated into protein

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25
Q

A nucleoside has…

A

Pentose (5C) sugar + organic base

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26
Q

A nucleotide has…

A

Pentose (5C) sugar + organic base + phosphate group(s)

Or

Nucleoside + phosphate group(s)

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27
Q

Pol II synthesises only stable RNA. True/False?

A

False

Pol II synthesises all RNA. Pol I and III synthesise only stable RNA

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28
Q

DNA polymerase has 3 important characteristics

A

Can only add to existing nucleic acids
Cannot start synthesis on its own
Requires an RNA primer to start replication

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29
Q

Enzymes can affect the equilibrium position of a reaction. True/False?

A

False

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30
Q

How do enzymes lower the activation energy of a reaction?

A

Bind to and stablise the transition state and provide alternative reaction pathways

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31
Q

Enzyme without a cofactor is called a…

A

Apoenzyme

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32
Q

Enzyme with a cofactor is called a…

A

Holoenzyme

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33
Q

Induced fit model describes enzyme-substrate interaction by…

A

Binding of substrate induces a conformational change in the enzyme, resulting in complementary fit

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34
Q

Trypsin and chymotrypsin work in the ____ and have an optimum pH of _

A

Small intestine, 7

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35
Q

What are isozymes?

A

Catalyse same reactions as enzymes but have different properties and structure

36
Q

CK is an isozyme. The M form is produced in ____ and the B form is produced in the ___. MB form is produced in the ___

A

Skeletal muscle, brain, heart

37
Q

Which enzymes carry out phosphorylation?

A

Kinases i.e. in the activation of zymogens

38
Q

What are zymogens?

A

Inactive precursors of an enzyme

39
Q

Where are trypsinogen and chymotrypsinogen formed? Why is it important they are produced inactive?

A

Pancreas

They would digest the pancreas if active

40
Q

Which enzyme activates trypsinogen? Where does this occur?

A

Enteropeptidase

Small intestine

41
Q

Vmax is?

A

The maximal rate of reaction at unlimited substrate concn

42
Q

Km is?

A

The concn of substrate which gives 50% maximal rate, i.e. 0.5Vmax

43
Q

A low Km means…

A

An enzyme only needs a little substrate to work at 0.5Vmax (it has high affinity)

44
Q

Vmax can be obtained from a Lineweaver-Burk plot by looking at the interesection with the X axis. True/False?

A

False

Intersection with X axis is Km; intersection with Y axis is Vmax

45
Q

In competitive inhibition, Vmax is ___ and Km is ___

A

The same, increased

46
Q

In non-competitive inhibition, Vmax is ___ and Km is ___

A

Decreased, the same

47
Q

Orthosteric enzymes follow M-M kinetics and the curve is shaped like a ____

A

Hyperbola

48
Q

Allosteric enzyme do not follow M-M kinetics and the curve is shaped like a ___

A

Sigmoid

49
Q

In the absence of a substrate, most enzyme subunits are in the inactive _ form. The presence of substrate shifts equilibrium from the inactive form to the active _ form

A

T (inactive), R (active)

50
Q

GLUT3 is located in the…

A

Brain

51
Q

GLUT5 is located in the…

A

Gut

52
Q

In glycolysis, glucose (6C) is converted into…

A

2 x pyruvate (3C each)

53
Q

In glycolysis, there is a net gain of how many ATP?

A

2 ATP

54
Q

The _, _ and _ reactions in glycolysis are control points (irreversible as they are very exergonic)

A

1st, 3rd and final

55
Q

3 enzymes involved in the glycolysis control points

A

Hexokinase, phosphofructokinase, pyruvate kinase

56
Q

We must reoxidise NADH to form __ in order to continue ATP synthesis after glycolysis

A

NAD+

57
Q

Pyruvate conversion to lactate occurs when?

A

Low oxygen - muscle cells work very hard to allow glycolysis to continue
NAD+ is regenerated by oxidation of NADH

58
Q

What is the substrate for the TCA cycle?

A

Acetyl-CoA

59
Q

Where does TCA cycle occur?

A

Mitochondria (mainly central matrix and then cristae)

60
Q

What is the fate of pyruvate before TCA cycle?

A

Enters mitochondria, where PDC catalyses oxidative decarboxylation of pyruvate to acetyl-CoA
2CO2 released in total

61
Q

Citric acid (6C) is formed by the combination of which 2 molecules?

A

Oxaloacetate (4C) + Acetyl-CoA (2C)

62
Q

How many cofactors are reduced in total in TCA cycle?

A

4 - 3x NAD+ and 1x FAD+

63
Q

GDP conversion to GTP is known as…

A

Substrate level phosphorylation

64
Q

Succinate hydrogenase uses FAD+ as a cofactor. It is the one enzyme of TCA cycle that is located in the central matrix. True/False?

A

False

It is the only enzyme located in the cristae - all others located in the central matrix

65
Q

Lipids are converted to ______ and then ____ which enters TCA cycle

A

Fatty acids, Acetyl-CoA

66
Q

Each turn of TCA cycle involves the uptake and release of how many carbon atoms, and in what form?

A

2C uptake as Acetyl-CoA, 2C released as 2CO2

67
Q

Glycolysis + PDC + TCA cycle reactions = _NADH, _H+, _FADH2

A

10NADH, 10H+, 2FADH2

68
Q

Each NADH and FADH2 molecule contains how many electrons?

A

2

69
Q

A -ve electron transfer potential means…

A

Substance is more likely to donate electrons than hydrogen

70
Q

What is the function of Co-enzyme Q?

A

Pick up electrons from Complex 1 or 2 and donate them to Complex 3

71
Q

Transfer of electrons through the respiratory chain is coupled to transport of _ from the mitochondrial matrix to the intermembrane space

A

H+

72
Q

Key point of oxidative phosphorylation:
Electrons from NADH and FADH2 reduce O2 to __
e- energy is used to pump protons from the matrix to the _____, causing matrix pH to ____
Protons follow their concn and flow across the membrane - this energy is used to phosphorylate ___ to ___

A

H2O
Intermembrane space, pH to increase (and intermembrane space pH to decrease)
ADP to ATP

73
Q

1 glucose molecule yields how many ATP molecules in total?

A

30-32 ATP

74
Q

Which bonds support a protein’s tertiary structure?

A

Disulphide bonding (-CH2-SH)

75
Q

What do free ribosomes produce proteins for?

A

Cytosol, nucleus, mitochondria

76
Q

What do bound ribosomes produce proteins for?

A

Membrane, ER, Golgi, Secretion

77
Q

GLUT1 is located in the…

A

Brain (low Km)

78
Q

GLUT2 is located in the…

A

Liver (high Km) and ß-cells (insulin independent)

79
Q

GLUT4 is located in the…

A

Muscle (insulin-dependent)

80
Q

What is the main enzyme controlling the rate of the glycolytic pathway?

A

PFK - Phosphofructokinase

81
Q

What is the Warburg effect?

A

Upregulation of anaerobic glycolysis in cancer cells

82
Q

Describe the movement of NADH from the cytosol to the intermembrane space

A

NADH used to generate malate from oxaloacetate and regenerates NAD+
Malate then gets transfered to mitochondrial matrix via transporters
Malate gets converted to oxaloacetate in the TCA cycle generating NADH and Fumarate

83
Q

Where do electrons from NADH enter the electron transport chain?

A

Complex I

84
Q

Where do electrons from FADH2 enter the electron transport chain?

A

Complex II (also part of TCA cycle)

85
Q

At which complex is water formed in the electron transport chain?

A

Complex IV

86
Q

Which electron transport chain complexes are also proton (H+) pumps?

A

Complex I, III & IV

87
Q

Which electron transport chain complex replenishes fumarate from succinate?

A

Complex II

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