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Biochemistry Flashcards

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1
Q

Name the three ways in which glucose is stored and transported. How are the latter two formed?

A

Monosaccharide, disaccharide, polysaccharide. Formed by a/B links

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2
Q

When are disaccharides particularly helpful?

A

When transporting glucose to target cells

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3
Q

In which two main structures may polysaccharides be found?

A

Cellulose and glycogen

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4
Q

What is the equation for Gibbs Free Energy?

A

dG = dH - TdS

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5
Q

Explain the concept of Gibbs Free Energy.

A

If positive (endergonic) the reaction is not favourable or spontaneous. If negative (exergonic) the reaction is favourable and spontaneous.

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6
Q

What is the difference between anabolism and catabolism?

A

Anabolism is addition, catabolism is release. Anabolism requires energy, catabolism releases it.

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7
Q

What is the name of the group of enzymes which phosphorylate ATP?

A

Kinases (ATPases too)

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8
Q

What is the name of the group of enzymes which dephosphorylate proteins?

A

Phosphatases

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9
Q

Describe the relationship between equilibrium constant and Gibbs free energy.

A

If K < 1, dG is more likely to be exergonic

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10
Q

Are hydrogen bonds straight or bent?

A

Straight

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11
Q

What is formed when oil enters water?

A

Micelles

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12
Q

Give the definition of ampipathic.

A

Has both hydrophobic and hydrophillic components

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13
Q

Describe the chemical structure of an amino acid.

A

N terminus (NH2) and C terminus (COOH)

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14
Q

What type of bond is formed when amino acids become proteins?

A

Peptide bonds.

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15
Q

What is the name of the equation which explains ion trapping?

A

Henderson-Hasselbalch

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16
Q

Give the Henderson-Hasselbalch equation.

A

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

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17
Q

What is a zwitterion?

A

An ion which has no overall charge, but more than one charged group, so has multiple titres

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18
Q

Name the three types of secondary protein structure.

A

A-helix, B-sheet, collagen triple helix

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19
Q

Describe tertiary structure.

A

Formed by R-group interactions. Fibrous is insoluble and strong, globular is soluble

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20
Q

Describe quaternary structure.

A

Multiple sub-units. If associated with other proteins, can lead to Parkinsons etc

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21
Q

Which amino acids provide turns in B-sheets?

A

Proline, glycine

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22
Q

What is the difference between the sugars in DNA and RNA?

A

DNA - deoxyribose (H), RNA - ribose (OH)

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23
Q

What are the two classifications of bases? Which does each fall into?

A

Purines - A, G. Pyramidines - C, T, U (three pyramid)

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24
Q

In which direction are nucleotides added to a growing DNA strand?

A

5’ to 3’.

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25
What is a nucleoside?
A sugar and a base
26
What is the name of the structure which can bind to nucleotides to prevent further DNA replication/growth?
An analogue
27
Describe the directions of the leading and lagging DNA strands.
Leading - 5' to 3'. Lagging - 3' to 5'. Okazaki fragments.
28
What are the three requirements to begin DNA replication?
Replication bubble, DNA polymerase, RNA primer.
29
What is the main difference (excluding structure) between beginning DNA and RNA synthesis?
RNA synthesis does not require a primer.
30
Is DNA replication conservative, semi-conservative, or dispersive?
Semi-conservative - One old strand and one new.
31
How do the main transcription factors begin RNA synthesis?
TATA binding protein (TBP) binds to TATA section. TFIID is a general factor
32
Describe the structure of the end of a new RNA chain being synthesised.
A hairpin with a C/G rich area, and a poly U site to terminate transcription
33
What is the main repair system for RNA synthesis?
3' to 5' exonuclease
34
Describe how stress intracellularly can cause formation of protein.
Stressor causes formation of stress response elements. Steroid + receptor in cytoplasm bind and cause transcription
35
Describe how transcription is degenerate.
Many amino acids have more than one codon.
36
Describe how transcription is unambiguous.
Each codon codes for only one amino acid
37
Which codon and amino acid always begin translation?
Methionine (Met) - AUG
38
Describe how pre-mRNA is converted into mRNA.
The end is cut and replaced with a poly A chain. G cap is added
39
Which chemical is responsible for directing aminoacyl-tRNA to the ribosome?
EF1alpha
40
Which chemical is responsible to regenerating EF1alpha?
EF-beta-gamma
41
Describe how tRNA collects the correct amino acid.
Aminoacyl-tRNA synthase directs the correct amino acid to the aminoacyl-tRNA
42
Name the three ribosome sites.
A - minoacyl, P - olypeptide, E - xit
43
Describe briefly how amino acids bind together in the ribosome, with reference to the three sites.
Aminoacyl binds to A site. Amino acid already bound to P site binds to amino acid on A site, releasing the tRNA from the P site. Ribosome shifts right, freeing the A space
44
Name the four base mutations.
Missense (swap), nonsense (STOP), silent, addition/deletion (frame shift)
45
Name the four chromosomal mutations.
Deletions, duplications, inversions, translocations
46
Proteins produced by free cytoplasmic ribsomes typically end up where?
Cytoplasm, nucleus, mitochrondria
47
Proteins produced by bound cytoplasmic ribosomes that are modified (not glycolysed) typically end up where?
Membrane, golgi, ER
48
What does glycolysation entail and where would it occur?
Carbohydrates/disulfides. Golgi or ER
49
Which condition may be caused by misfolding of glycolysed proteins?
Emphysema
50
Which condition may be caused if the golgi fails to sort glycolysed proteins?
Mucolipidosisil
51
How do enzymes affect equilibrium rate?
Rate at which equilibrium is reached is increased.
52
Describe the pathology of glycogen storage disease.
An enzyme deficiency when converting glucose/glycogen to glucose-6-phosphate.
53
What are cofactors and coenzymes?
Substances other than the substrate that must be present for enzyme function. Cofactors are metallic, coenzymes are metallic
54
Name the two different types of metallic enzymes.
Apoenzyme (no cofactor), holoenzyme (cofactor)
55
Give examples of coenzymes.
CoA, NAD, FAD
56
Name the three main proteases.
Chymotrypsin, trypsin, elastase
57
What is an isozyme? Give examples.
A different form of an enzyme. Lactic acid dehydrogenase, creatine kinase.
58
Give the main form of reversible enzyme activation.
Phosphorylation
59
Give the main form of irreversible enzyme activation.
Covalent modification (i.e. cutting)
60
Consider the curve for enzymatic conversion [substrate] against velocity. What is [Km]?
The concentration of substrate at which rate is 50% of its maximum (Vmax).
61
If an enzyme has a high [Km], is it efficient or not?
Not efficient - more is needed for higher rate
62
What is [Km] otherwise known as?
The Michaelis constant
63
What is the main formula for [Km]?
[Km] = (K-1 + K2)/K1
64
What is the name of the equation set that allows calculation of [Km] and Vmax? What is the name of the graph when this is plotted?
Michaelis-Menten, and Lineweaver-Burk plot
65
Why is it important the enzyme hexokinase has a low Km?
Must work quickly with the glucose in the blood
66
Compare a normal Lineweaver-Burk plot with one with a competitive inhibitor.
Same Vmax (y intercept), competitive has higher gradient
67
Compare a normal Lineweaver-Burk plot with one with a non-competitive inhibitor.
Same Km (x intercept), non-competitive has lower gradient
68
Which enzyme sites do inhibitors use?
Competitive - orthostatic. Non-comp - allosteric
69
What does a sigmoidal curve indicate?
Co-operativaty
70
How does glucose enter the cell?
Na+/Glucose symporters (GLUT 1 - 5)
71
Describe the substrate entry reaction in glycolysis. Describe the ATP reaction.
Glucose -> glucose-6-phosphate by hexokinase. ATP -> ADP + Pi
72
Describe the rate limiting step of glycolysis.
Fructose-6-phosphate to fructose-1,6-biphosphate, by phosphofructokinase
73
Which cancer drug can inhibit hexokinase?
2-deoxyglucose
74
Which substances inhibit PFK?
ATP, citrate, H+
75
In glycolysis, what is F-1,6-bP converted to?
DHAP AND G-3-P
76
Describe what occurs when G3P is converted to 1,3-bPG in glycolysis.
2 1,3-bPG are produced. 2 NAD+ are converted to NADH
77
Describe what occurs between the conversion of 1,3-bPG and phosphophenol pyruvate.
(2x) ATP produced, 2x H2O produced
78
Which substance can inhibit the conversion of G3P to 1,3-bPG?
3-bromo pyruvate
79
Which enzyme converts phosphenol pyruvate to pyruvate? What is the byproduct?
Pyruvate kinase - ATP.
80
What are the end products of glycolysis?
2 x pyruvate, 2 x NADH, 2 x H2O, 4 x ATP
81
How is pyruvate converted to lactic acid and vice versa?
NADH -> NAD+ (loses electron) and vice versa
82
Which substance stimulates the conversion of lactic acid to pyruvate?
Dichloroacetate
83
What substance is required to convert pyruvate to intermediates of the CAC?
Oxygen
84
Name the intermediates of the CAC.
Acetyl CoA -> citrate -> 5C -> succinate -> fumerate -> malate -> oxaloacetate
85
Where does the CAC occur?
The mitochondrial matrix
86
Which enzyme converts succinate to fumerate? What is the byproduct?
Succinate dehydrogenase. FAD -> FADH2
87
What may be the negative effect of a lack of fumerase?
Malignant or benign tumours
88
Which two non-pyruvate substances enter the CAC, and where?
Lipids (acetyl CoA), amino acids (5C/fumerate)
89
What are the end products of the CAC?
10 NADH, 2 FADH2, 6ATP
90
Describe the purpose of NADH and FADH2 in the electron transport chain?
Provide H+ and e-. H+ is pumped into the high concentration H+ inner membrane by e-.
91
What accepts the H+ and e- from the electron transport chain?
Oxygen (producing water).
92
How is ATP produced in the electron transport chain?
H+ pumped through ATP synthase
93
Describe the structure of ATP synthase.
Stator - A, B, alpha, beta | Rator - C, gamma, oopsilon
94
Name the three main components of the malate-aspartate shuttle.
Malate -> oxaloacetate -> aspartate
95
What is the main purpose of the malate-aspartate shuttle?
To provide NADH in the mitochondria (NADH is oxidised in glycolysis to provide an electron)
96
Describe why pumping H+ through ATP synthase produces energy.
Creates a proto-motive force (by difference in pH and voltage)
97
What are green proteins that contain a haem group called?
Cytochrome proteins
98
Which two main factors determine ATP production?
P/O ratio, malate-aspartate shuttle
99
How many ATP are produced from a single glucose?
30-32
100
What is the name of the inner mitochondrial matrix?
Cristae

PRINCIPLES (10 decks)

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