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Biochemistry Flashcards

1
Q

What is the linkage found in cellulose? Can it be broken down by polysaccharides?

A

B(1,4) linkage.

No.

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2
Q

What is the linkage found in glycogen for branching?

A

a(1,6) linkage

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3
Q

What is the linkage found in glycogen for linear residues?

A

a(1,4) linkage

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4
Q

What is the product of pentose phosphate pathway for oxidation of glucose?

A

Ribose-5-phosphate

** For nucleotide synthesis and DNA repair

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5
Q

What is the product of anaerobic glycolysis? What is the process called?

A

Lactate.

Fermentation - rapid but inefficient and less ATP

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6
Q

What is the product of aerobic glycolysis? What is the process called?

A

Pyruvate.

Oxidation.

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7
Q

Does glycolysis use substrate phosphorylation or oxidative phosphorylation?

A

Substrate

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8
Q

GLUT 1, 2 and 3. Which are found in the brain and liver? What are their KMs relative to each other?

A

Brain - 1,3 - Low KM (Still transports effeciently at low glucose conc.)
Liver - 2 - High KM

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9
Q

What component/ nutrient from our diet gives us NADH?

A

Niacin

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10
Q

At which part of the cell does glycolysis take place?

A

Cytosol

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11
Q

How many ATP does glycolysis use and yield? How many NADH yielded?

A

2 ATP used

4 ATP and 2 NADH + 2 H+ yielded

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12
Q

In the first step of glycolysis, glucose is converted into glucose-6-phosphate via which enzyme?

A

Hexokinase

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13
Q

Aldolase acting on Fructose 1,6 biphosphate yields?

A

2 interconvertible 3C molecules

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14
Q

What are the 3 enzymes that catalyses the control points in glycolysis?

A

Hexokinase (1st; ATP-dependent)
Phosphofructokinase (3rd; ATP-dependent)
Pyruvate kinase (9th; ATP-yielding)

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15
Q

Does ADP or AMP have a stronger influence in promoting phosphofructokinase?

A

AMP.

ADP can still be broken down to give AMP and Pi by adenylate kinase

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16
Q

What is the effect of Fructose 2,6-bisphosphate on Phosphofructokinase?

A

Stimulates its action.

Fructose 2,6-biphosphate levels will be high when glucose concentration is high

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17
Q

What are the 3 inhibitors of glycolysis?

A

ATP (energy abundant)
Citrate (slows entry into TCA cycle)
H+ (excess lactic acid)

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18
Q

What happens when there is lack of oxygen for pyruvate to enter the TCA cycle?

A

NADH will be used to ferment pyruvate into lactic acid

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19
Q

What does NADH become when it converts pyruvate to lactic acid?
What are the 2 fates of this product?

A

Becomes NAD+.

  1. Decarboxylates Pyruvate to Acetyl-CoA
  2. Used in 5th step of glycolysis to regenerate NADH
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20
Q

What is the Warburg effect?

A

Preferential anerobic glycolysis (Lactic acid) over aerobic glycolysis in cancer cells

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21
Q

Does hexokinase in cancer cells have a high or low KM?

A

Low

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22
Q

What are the 3 advantages and 2 disadvantages of the Warburg effect?

A

Advantages: Rapid energy production, rapid growth, supports other pathways for nucleotide synthesis
Disadvantages: Inefficient ATP synthesis, High glucose consumption (weight loss)

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23
Q

Where is glycolysis targeted to treat cancer?

A

At or just after rate-limiting/ control points

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24
Q

How is NAD+ regenerated?

A

Oxidative metabolism of pyruvate via Pyruvate Dehydrogenase Complex (PDC) yielding Acetyl-CoA as well

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25
Q

Where does the TCA cycle take place?

A

Mitochondria matrix

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26
Q

What is the H+ gradient across the inner mitochondria membrane?

A

Inwards as the matrix is more negative

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27
Q

What kind of reaction does Pyruvate Dehydrogenase Complex (PDC) result in?

A

An irreversible one; thus it is a rate-limiting step

**Acetyl-CoA cannot go back to becoming pyruvate

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28
Q

How many reactions does one TCA cycle have?

A

8

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29
Q

Where are the enzymes of the TCA cycle located at?

A

All in matrix except succinate dehydrogenase (6th step) (integrated in inner mitochondria membrane)

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30
Q

Metabolites of the TCA cycle can exit the cycle to participate in what kind of reactions?

A

Anabolic

Making fatty acid from citrate

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31
Q

What kinds of products can give rise to Acetyl-CoA to enter the TCA cycle?

A

Glucose, fatty acids, amino acids

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32
Q

What are the positive (5) and negative (2) controls of the TCA cycle?

A

Positive: ATP, NADH, Acetyl-CoA, Succinyl-CoA, Citrate
Negative: ADP, NAD+

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33
Q

What are the 4 control points of the TCA cycle?

A

Formation of acetyl CoA, Citrate, a-ketoglutarate, succinyl-coA

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34
Q

What is the net yield from glycolysis and TCA cycle from 1 glucose molecule?

A

Glycolysis: 2 ATP (4-2), 2 NADH, 2H+

TCA (2 cycles): 2 GTP, 8 NADH, 8 H+, 2 FADH2, 6 CO2

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35
Q

What is the inheritance pattern of a PDC deficiency?

Which gender results in carrier and which results in a stillborn?

A

X-linked.
Daughter - carrier
Son - stillborn

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36
Q

Where will the more severe phenotype manifest in in PDC deficiency?

A

Energy-demanding tissues (E.g. Brain - neurological and developmental symptoms)

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37
Q

What is the inheritance pattern for Fumurate Hydratase (TCA cycle enzyme)? Which disease is it associated it?

A

Autosomal dominant

Associated with Hereditary Leiomyomatosis (smooth muscle tumours) and Renal Cell Cancer (HLRCC)

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38
Q

What are the 4 stages of intracellular metabolism?

A
  1. Ingestion/ Absorption
  2. Acetyl-CoA formation
  3. Acetyl-CoA oxidation (TCA)
  4. Electron transport and oxidative phosphorylation
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39
Q

Where does oxidative phosphorylation take place?

A

Inner mitochondria membrane

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40
Q

What are electrons from NADH and FADH2 used reduced? What is the energy from this reduction used for?

A

O2 to H20.

Energy used for pumping H+ to intermembrane space against gradient

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41
Q

What are 2 ways in which the 2 NADH from glycolysis can cross the inner mitochondria membrane?

A
  1. Malate-Aspartate shuttle (NADH generated again)

2. Glycerol-3-phosphate shuttle (NADH oxidized to reduce FAD to FADH2)

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42
Q

Reduced form of molecules have a lower or higher affinity for electrons?
Does O2 accept or donate electrons?

A

Lower - thus they tend to donate; thus eventually oxidised

O2 accepts electrons thus eventually reduced to H2O

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43
Q

What is electron transfer potential and phosphoryl transfer potential?
What is converted to what?

A

ETP: Redox potential of compound/ how readily they donate electrons
PTP: Free energy change to hydrolyse ATP

ETP of co-factors are converted to PTP of ATP

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44
Q

Are the proton pumps used in the ETC and phosphorylation the same?

A

No

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45
Q

How many complexes does the ETC have and where are they located?

A

4.

Inner mitochondrial membrane

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46
Q

Which ETC complex does electrons from NADH and FADH2 enter?

A

e- from NADH enters at complex I

e- from FADH2 enters at complex II (part of TCA cycle)

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47
Q

What is the trend of the ETC as electrons are being passed down?

A

Complexes become more oxidizing/ positive redox potentia/ accepts e- more readily

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48
Q

Cytochromes in the ETC possesses what groups to take and release electrons?

A

Haem groups containing Fe2+

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49
Q

Which ETC complex does not pump H+ out?

A

Complex II

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50
Q

What happens to the H+ that are pumped to the intermembrane space?

A

Flows back down electrochemical gradient via ATP synthase

*Electro because matrix is more negative from pumping protons out

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51
Q

What are the 3 components of ATP synthase and what 2 substrates are needed to synthesize ATP?

A

Proton channel, Stator (does not rotate, ATP forms here), Rotor (changes conformation of stator as proton flows)

Substrates: ADP, Pi

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52
Q

What are 3 substances that can inhibit electron transfer from complex IV to O2?
What is the consequence?

A

Cyanide, Azide, Carbon monoxide

No energy to pump protons out -> no gradient -> no ATP synthesis

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53
Q

What do brown adipose tissue contain more than white fat?

A

Uncoupling protein (UCP)/ Thermogenin and mitochondria

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54
Q

What is non-shivering thermogenesis?

A

Heat generation via flowing of protons down UCP-1 (Proton leak) instead of ATP synthase

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55
Q

What is UCP-1 activated and inhibited by?

A

Activated by fatty acids (Cold -> NA -> B-adrenoceptors -> lipolysis)
Inhibited by nucleotides

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56
Q

How does artificial uncoupler 2,4-DNP (Proton leak) cause weight loss?

A

By increasing metabolic rate via thermogenesis but can cause overheating

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57
Q

What does ecstasy (MDMA) target? Where is this found at?

A

Targets UCP-3 at skeletal muscle.

Can result in sustained hyperthermia and rhabdomyolysis

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58
Q

What is the P/O ratio of NADH and FADH2?

*# of Pi incorporated into ADP per atom of oxygen used

A

NADH: 2.5
FADH2: 1.5 (less yield as electrons only enters from complex II)

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59
Q

What strongly influences P/O ratio?

A

Uncoupling protein activity

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60
Q

What are the 2 factors that influences the final ATP yield per complete oxidation of 1 glucose molecule?
What is the final ATP yield?

A

P/O ratio and shuttle used to transport cytoplasmic NADH into mitochondria matrix.

32 ATP if malate-aspartate shuttle used (no change in # of NADH)

30 ATP if glycerol-3-phosphate shuttle used (2 glycolytic NADH to 2 FADH2)

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61
Q

What is the configuration of a heme group?

A

Planar

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62
Q

What is electronegativity?

A

Attractive force that atomic nucleus exerts on electrons within bond

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63
Q

What are the 3 characteristics of a receptor to hormones/ enzymes?

A

Recognition, communication & specificity

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64
Q

How many carbons does glucose have?

A

6Cs (Ringed hexose)

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65
Q

What is the relation between energy of reactant and products in an exergonic reaction?
Is Gibb’s free energy + or -?

A

Reactant less energy than product

Gibbs: negative

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66
Q

What is the relation between energy of reactant and products in an endergonic reaction?
Is Gibb’s free energy + or -?

A

Reactant more energy than product

Gibbs: positive

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67
Q

When does a reaction occur spontaneously (does not need energy)?

A

When Gibb’s free energy is negative

Tend to go towards 0 (equilibrium)

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68
Q

What determines if Gibb’s is + or -?

A

Initial concentration of reactant

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69
Q

What is the universal gas constant?

A

8.3J/Kmol

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70
Q

If Gibb’s energy is close to 0, what does it say about the reaction?

A

It is readily reversible

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71
Q

How do cells carry out unfavorable processes such as active transport and anabolism (Gibbs: +)?

A

By coupling with favourable processes (Gibbs: very negative) such as ATP hydrolysis

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72
Q

How many carbons does the sugar group have in ATP?

A

5Cs (Ribose)

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73
Q

What is the name of the high energy bond that links phosphates together in ATP?

A

Phospho-anhyride linkage (-P-O-P)

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74
Q

Why is ATP less stable than ADP?

A

Due to electrostatic repulsive strain from close proximity of negative charges between phosphate groups

**Thus usually there is a higher concentration of ADP

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75
Q

How is ATP regenerated in muscle cells?

A

By reacting ADP with creatine phosphate to yield creatine and ATP

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76
Q

ATP concentration is kept under?

A

<10mM

Excess broken down –> energy release

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77
Q

Can reactions with negative Gibb’s energy be used as control points?

A

No, it’ll cause the reaction to occur more spontaneously

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78
Q

How many pyruvates are produced per glycolysis?

A

2 pyruvates thus 2 acetyl-CoA will be formed

1 glucose = 2 TCA cycles

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79
Q

What is the configuration of H-bonds?

A

Linear

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80
Q

What are 3 H-bond acceptors?

A

F, N, O

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81
Q

What are the 2 stereoisomer forms of amino acids?

*Non-superimposable mirror image

A

D and L

*L found in humans

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82
Q

What structure does amino acids have?

A

Tetrahedral

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83
Q

What is the carbon at the centre of the amino acid known as?

A

Alpha carbon

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84
Q

What catalyses the condensation of 2 amino acids?

A

Peptidyl transferase

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85
Q

How are peptide chains read?

A

From N to C terminus

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86
Q

What are the characteristics of a peptide bond (5)?

A

Planar
Strong
Rigid
Rotatable between alpha carbon and C and alpha carbon and N
Resonant (partial double bond from electrons from N and C)

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87
Q

What determines the characteristic of an amino acid?

A

The R group

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88
Q

What is the Ka and pKa of a strong acid?

A 
High Ka (Higher ratio of ionized form)
Low pKa
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89
Q

What is the formula for pH?

A

-log10 [H+]

90
Q

What is the formula for the Henderson-Hasselbach equation?

A

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

91
Q

When [HA] = [A-], what is pKa - pH?

A

0 as pKa = pH.

Shows that unionised:ionised ratio is 1

92
Q

When pH = pKA, what can the solution act as?

A

A buffer to resist change of pH when moderate amounts of acid or base is added

93
Q

What is the isoelectric point/ zwitterion?

A

0 net charge, charges on side groups cancel out

94
Q

How many pKa values does uncharged amino acids have?

A

2 due to having 2 groups (N and C)

**with isoelectric point in between

95
Q

What is the primary structure of proteins?

A

Amino acid residue sequence

96
Q

What is the secondary structure of proteins?

A

H-bonded 3D arrangement of polypeptide chains and only considers backbone of polypeptide

97
Q

How often does H-bond occur between C=O and N-H in an alpha helix?

A

Every 4 residues

98
Q

Which amino acid residue breaks alpha helices?

A

Proline - introduces a destabilising kink which can allow another secondary structure to start

99
Q

What happens to the polypeptide backbone in Beta sheets? And what are the 3 ways that the sheets can be arranged in?

A

Almost completely extended.

Parallel, anti-parallel, zig-zag (pleated sheet; alpha-carbon comes in and out of plane)

100
Q

Which 2 amino acids introduces turns between strands?

A

Glycine and Proline

101
Q

Where are Collagen triple helix found in?

A

Bone and connective tissue (Very strong)

102
Q

What is the structure of a collagen triple helix?
What is the bond found between chains?

What is the sequence of amino acid in a collagen triple helix?

A

3 left handed helical chains twisted around each other forming a right handed superhelix (Tropo-collagen)
- Stabilised by H-bonds between chains by hydroxylysine and hydroxyproline

Repeating sequence of X-Y(Proline or hydroxyproline)-Gly in all strands

103
Q

What is needed to make hydroxyproline? What is the consequence if there is a deficiency?

A

Vitamin C is needed to hydroxylate proline to form inter-chain H-bonds
Scurvy due to weakened collagen –> bleeding gums, discolouration

104
Q

What is the tertiary structure of proteins?

A

Arrangement of all atoms of a polypeptide in space with local regions of distinct secondary structure

105
Q

Which amino acid oxidises SH-SH to form covalent disulfide bonds?

A

Cysteine

106
Q

What are the 2 types of protein seen in tertiary structures of protein?

A

Fibrous and Globular

107
Q

What are fibrous proteins?

Give 2 examples

A

Polypeptide chain organised parallel along a single axis either as long fibers or large sheets
E.g. Keratin, Collagen

108
Q

What are 2 characteristics of fibrous proteins?

A

Mechanically strong, insoluble in water and slightly in salt solution

109
Q

Are Collagen triple helix water-soluble?

A

Yes

110
Q

What are globular proteins?

Give 2 examples

A

Folded into a spherical shape with polar side chains facing out and non-polar side chains facing in
E.g. Hb and Myoglobin

111
Q

What is the solubility of globular proteins?

A

Soluble in water and salt solution

112
Q

What is the SNP involved in sickle-cell anaemia?

A

E6V

Hydrophilic glutamic acid substituted with hydrophobic valine

113
Q

What happens at low oxygen condition in sickle-cell anaemia?

A

Haemoglobin polymerises resulting in a rigid, sickle-shaped RBC which can occlude flow in capillaries

114
Q

How are polypeptide chains folded?

A

Spontaneously (slow and erroneous)

Aided by chaperones

115
Q

What are prions?

1 example of a disease that it can cause.

A

Misfolded proteins that can misinform the folding of normal variant proteins - can aggregate to form amyloids
E.g. Creutzfeldt–Jakob disease (CJD)

116
Q

What are quarternary structures of a protein?

Give an example and how many subunits it has.

A

Has >1 polypeptide chain (and many subunits)

E.g. Hb has 4 subunits (2a and 2B) each with own haem group to bind to 1 O2

117
Q

What can heat, extreme pH, detergents, reducing/ thiol agents cause?

A

Protein denaturation

**Reducing agents disrupts disulfide bonds

118
Q

What happens when 1 O2 binds to Hb?

A

Affinity of other subunits to O2 increases as conformation changes (Allosteric regulation & cooperative binding)

119
Q

DNA replication is required before transcription.
T/F?
What is the product of transcription?

A

False.

mRNA

120
Q

What are the 2 differences between DNA and RNA?

A

RNA vs DNA

  1. Ribose and Deoxyribose
  2. Uridine and Thymine
121
Q

What are purines and pyrimidines?

A

Purine: A, G
Pyrimidine: U, T, C

122
Q

What is the bond linking free 3’OH group of the ribose to 5’ triphosphate called?
Does this take energy?

A

Phosphodiester bond

Yes.

123
Q

Which direction to read DNA in?

A

5’ to 3’!!!

124
Q

How are viral DNA targeted to terminate elongation?

A

Via thymidine analogues (lack free 3’OH group) where viral reverse transcriptase has a higher affinity for.

125
Q

How are the strands of a DNA double helix arranged?

What faces inside and outside?

A

Anti-parallel.

Sugar phosphate backbone outside and base pairs inside

126
Q

What force holds nucleotide base pairs together?

What is the combination of base pairing?

A

H-bond.
A to T/ U
C to G

127
Q

When is DNA replication needed?

What model does it operate on?

A

Before cell division to have complete complement genome for daughter cells.
Semi-conservative model (Each parental strand synthesizes a complementary strand and forms the double helix together)

128
Q

What enzyme is needed for DNA replication?

What is required before that to start?

A

DNA Polymerase.

Needs RNA Primer does DNA Pol only adds to existing nucleic acids

129
Q

How many origins of replication does eukaryotes have?

What direction does it go in?

A

Many thus replication can start simultaneously

Bidirectional to over more area

130
Q

What direction does replication occur in?

A

3’ to 5’!!

Opposite from how DNA is read!!

131
Q

What happens at the start of replication? (4)

A

Formation of replication bubble and bidirectional fork
DNA helicase unwinds double helix and stop it from rewinding
Single strand binding protein keep template strand separated
DNA primase to synthesize RNA primer

132
Q

What are the 2 template strands in DNA replication called?

A

Leading and lagging strands

133
Q

What direction does leading strand go in in DNA replication?

A

Follows fork movement.

Has free 3’ end thus elongates complementary DNA smoothly

134
Q

What are the strands replicated in short segments in the lagging strand called?
What direction does it occur in?

A

Okazaki segments

Done backwards in bits with short RNA primers (degraded after and gaps filled in by DNA polymerase)

135
Q

What other activity does DNA polymerase have other than replication?

A

3’ to 5’ exonuclease activity (backwards) for proofreading by remove incorrect nucleotides

136
Q

Which nucleic acids can have stem loops in them?

A

RNA, from intramolecular base pairing

137
Q

What are the 3 types of RNA in order of abundance?

A

rRNA > tRNA (carries amino acid) > mRNA

138
Q

What structure does tRNA have?

What is the 3 nucleotide segment in the tRNA called?

A

Seen as cloverleaf when 2D.

Anticodon base-pairs with specific codon on mRNA.

139
Q

How many types of RNA Polymerase does eukaroytes and prokaryotes have?
Which type synthesizes all mRNA in eukaroytes?

A

Eukaryotes: 3 types, RNA Pol II synthesizes all mRNA
Prokaryotes: 1 type

140
Q

How many DNA strands are used as template in replication and transcription?

A

Replication both strands (Leading and lagging).

Transcription only 1 strand.

141
Q

What does RNA polymerase bind to?
Is RNA primer needed?
What direction does it move?

A

Promoter/initiation site along with other transcription factors.
No.
3’ to 5’

142
Q

Relation of transcript to template and coding strand?

A

Template: Complementary and anti-parallal
Coding: Almost identical except U and T bases

143
Q

Does the coding or template strand take part in transcription?

A

Only template strand

144
Q

What is the TATAbox and which protein binds to it first?

A

RNA Pol II specific promoter region 25 nucleotide upstream of initiation site.
TATA-binding protein which is part of TFIID as a platform to allow for RNA Pol II and other transcription factors to bind.

145
Q

Why does TFIID remain at promoter when transcription is occuring?

A

Allow for new initiation complex to assemble thus transcription takes place at low, basal rates (constitutive).
No effect on RATE of transcription.

146
Q

What kind of transcription factors does the initiation stage of transcription require?
Does the order of assembly matter?

A

General transcription factors.

Yes.

147
Q

In what direction does the replication and transcription bubble move in?

A

Replication bubble: Bidirectional

Transcription bubble: 1 direction

148
Q

As the transcription bubble moves what happens to the DNA?

A

DNA unwinds in front and rewinds behind

149
Q

What happens during the termination stage of transcription? (3)

A

RNA makes stem-loop structure with a stretch of Us behind
Specific enzymes recruited to cleave RNA
RNA Pol dissociates

150
Q

What are the 3 stages of transcription?

A

Initiation
Elongation
Termination

151
Q

What kind of transcription factors are needed for regulation?

A

Specific transcription factors binding to specific DNA seq near promoter
*General TFs for initiation

152
Q

What are 3 types of specific transcription regulators?

A
  1. Enhancers
  2. Repressors
    * Both can be far away from promoter; E.g. DNA bending brings activator protein bound to enhancer to the transcription complex
  3. Stimuli-specific TF
    * Regulatory protein binds to stress response element to transcribe specific genes involved in stress response
153
Q

Homodimers of steroid receptors bind to what in the DNA?

A

Steroid response element

154
Q

What happens to the mRNA before it proceeds to translation? (3)

A

Processing to become mature.

  1. Spliceosomes splice out introns
  2. Polyadenylation - add Poly(A) tail after cleaving 3’ sequence away (Stretch of Us)
  3. 5’ capping with modified 5’ GTP cap to prevent degradation by exonuclease
155
Q

Where does translation and transcription occur?

In what order does in order in eukaryotes and prokaroytes?

A

Transcription in nucleus, translation in cytosol
In eukaroytes, sequential
In prokaryotes, simultaneous

156
Q

What are the 3 characteristics of the genetic code?

A
  1. Degenerate - many amino acids have >1 codon
  2. Unambiguous - but each codon only codes for 1 amino acid/ stop
  3. Nearly universal
157
Q

What is the start and stop (3) codon?

A

Start: Methionine (AUG)
Stop: UGA, UAG, UAA

158
Q

How many reading frames does translation have?

A

3

159
Q

What happens during the initiation stage of translation? (6)

A

40S (small) subunit with initiation factors bind to 5’ mRNA
Scans until AUG found (ATP dependent)
Initiator tRNA base pairs with start codon
60S (large) subunit joins (ATP dependent)
Initiation factors released
tRNA on P site

160
Q

Where are the tRNA binding sites located at? Where are they called?

A

60S subunit

A, P, E

161
Q

What are the ribosomal subunits for prokaryotes and eukaryotes?

A

Prokaryotes: 50S, 30S
Eukaryotes: 60S, 40S

162
Q

What happens during elongation stage of translation (6)?

A

EF-1a brings aminoacyl-tRNA to A site
EF released from tRNA (GTP-dependent)
Peptidyl transferase catalyses peptide bond formation between amino acid of A and P site
Peptide chain then shifted to A site
EF-2 moves ribosome along mRNA by 1 triplet (GTP-dependent)
Empty tRNA moves from P to E site and exits while tRNA with peptide chain moves from A to P site

163
Q

What is the role of aminoacyl-tRNA synthetase?

A

Highly specifically binds activated amino acid to correct tRNA

164
Q

When is EF-1a available to pick up aminoacyl-tRNA?

A

When it is GTP bound

165
Q

When and where does translation terminate?

A

At A site.

When stop codon is encountered.

166
Q

What happens when a stop codon is encountered?

A

Release factor binds to it (GTP-dependent) as there is tRNA for stop codons
Polypeptide cleaved off tRNA
Complex dissociates

167
Q

What are polysomes?

A

Multiple ribosomes bound at different sites of mRNA producing multiple growing peptide chains

168
Q

What kind of mutation have changes to amino acid sequence?

A

Missense

169
Q

What kind of mutation results in a truncated polypeptide?

A

Nonsense - premature stop codon

170
Q

What are the 5 DNA/ amino acid mutations?

A
  1. Point (single base change)
  2. Missense
  3. Nonsense
  4. Silent (no change in amino acid sequence due to degenerate genetic code where a few codons can code for 1 amino acid)
  5. Frameshift (Add/ Del of bases)
171
Q

What are the 5 chromosomal mutations?

A 
Deletion
Duplication
Inversion
Insertion
Translocation
172
Q

What happens to the polypeptide after translation? (3)

A
  1. Targeting/ transport
  2. Post-translation modification
  3. Degradation if damaged/ unwanted
173
Q

What are the 2 types of ribosomes in the cytosol?
What kinds of proteins do each translate?
When are they translocated?

A
  1. Free - proteins for cytosol, nucleus, mitochondria
    - translocated post-translation
  2. Bound on RER - proteins for plasma membrane, ER. Golgi apparatus, secretion
    - translocated co-translation
174
Q

What is hereditary emphysema due to?

A

Misfolding of a1-antitrypsin in ER

175
Q

What is the inheritance pattern of inclusion cell disease (mucolipidosis)? What is the pathology?

A

Autosomal Recessive.
Proteins destined for degradation at lysosome not sorted properly at golgi apparatus -> ends up being secreted.
Death before 8.

176
Q

What do enzymes do?

A

SPEEDS UP RATE of reaction by stabilizing transition/ intermediate state of a reaction via an alternate pathway with lower activation energy
***No effect on equilibrium position, start and end point does not change

177
Q

Are all enzymes proteins?

A

No, some are ribozymes (RNA)

178
Q

What kind of environment do enzymes work in?

A

Body temp
Neutral pH
Aqueous solution

179
Q

Does enzyme affect the start and end point of a reaction?

A

No

180
Q

How much enzyme is used up in a reaction?

A

Enzymes are not consumed

181
Q

What is the activation energy?

A

Energy of reactant to peak.

182
Q

How can substrates be forced closer to react?

A

Heat (Kinetic energy) or pressure (compact space)

183
Q

What does non-functional Glucose-6-phosphatase result in?

A

Glycogen storage disease. (Von Gierke’s disease)

Hinders glycogenolysis - cannot produce glucose

184
Q

What are co-factors?

A

Inorganic metal ions

185
Q

What are co-enzymes?

A

Organic carriers that transiently associate with enzymes; able to regenerate/ recycle
E.g. Vitamins (Redox reactions, group transfers)

186
Q

What are cofactors tightly bound to enzymes called?

1 example.

A

Prosthetic group.

E.g. Haem (Metallo-protein)

187
Q

What is the term for an enzyme with and without a cofactor?

A

With - holoenzyme

Without - Apoenzyme

188
Q

What are the 2 models for specific binding of substrate to enzyme?

A 
Lock and key (Complementary shape)
Induced fit (enzyme changes conformation to match substrate)
189
Q

How are the active sites of the 3 pancreatic serine proteases like?
Chymotrypsin, Trypsin, Elastase

A

Chymotrypsin - hydrophobic pocket
Trypsin - lined with negatively charged aspartic acid
Elastase - small hydrophobic pocket

190
Q

What are physical factors that influences rate of reaction?

A

Temp
pH
*To optimal levels

191
Q

What are isozymes?

1 example?

A

Isoforms of enzymes with differenr properties and structure but catalyses same reaction (at slightly different condition)
E.g. LDH 1-5

192
Q

Is pyruvate reduced or oxidised to lactate?

What are the 2 substances needed to catalyse the reaction?

A

Reduced
By NADH and LDH-5

**Same enzyme used to oxidise lactate back to pyrvuate but LDH-1

193
Q

What can be used to stabilise charge?

A

Metal ions

194
Q

What transcriptive mechanism does hypoxia result in?

A

Activation of hypoxia sensitive TF binding to hypoxia response element which encodes for LDH-5 (Promotes pyruvate reduction to lactate)

195
Q

What are the 3 isotypes of CK and where are they found at?

A

M - Skeletal muscle
B - Brain
MB - Heart (heterodimer)

196
Q

What does phosphorylation (covalent modification) of enzyme result in? What helps to carry it out?
Is it reversible?

A

Activation and inactivation of enzyme.
Carried out by protein kinase (transfers phosphate from ATP - uses energy)
Reversible

197
Q

What does irreversible covalent modification of enzyme result in?
1 example.

A

Activation of enzyme.
E.g. Zymogens irreversibly activated by proteolytic enzymes to active enzymes via covalent bond cleavage (GI enzymes, coagulation cascade, fibrinolysis)

198
Q

What is [KM]

A

Substrate concentration at 50% Vmax

199
Q

What is the Michaelis Menten equation?

A

Initial reaction rate, Vo

Vo = Vmax [s] / (KM + [s])

200
Q

Does Vo ever reach Vmax?

A

No, kinetics is not linear (asymptote)

201
Q

What is the double reciprocal plot of Vmax vs [s] called?

What does it help to determine? (2)

A

Lineweaver Burk Plot

Helps to accurately determine KM and Vmax by becoming linear

202
Q

Relation between low KM and 50%Vmax?

A

low KM: low [s] needed for enzyme to work at 50% Vmax

203
Q

2 enzymes that plateau off at the same Vmax but with different speed will have?

A

Different KMs

204
Q

In the Lineweaver Burk Plot, smaller values will be ___ to/from the origin (0,0)?

A

further

205
Q

Isoenzyme Hexokinase in RBCs have a significantly lower KM than glucokinase in liver/pancreas.
Both converts glucose to G6P by hydrolysing ATP.
What does the KM difference help each enzyme to do?

A

Hexokinase - energy production maintained even at low [glucose]
Glucokinase - more sensitive to rise and fall of glucose thus activating insulin if [glucose] >5mM

206
Q

Is the KM high/low for Prolyl hydroxylases (PHD)?

What happens in hypoxia?

A

High KM - allows for O2 sensing

Hypoxia initiation factor activatd –> dimerizes and transcribe genes to survive hypoxia (angiogenesis, RBC synthesis)

207
Q

Where/Who does Monge’s disease occur?

What happens to haematocrit levels and O2 regulation?

A

Native population at high altitudes.

High haematocrit and loss of O2 regulation of Epo production (for RBC synthesis)

208
Q

What is Von Hippel Lindau (VHL) syndrome?

What is 1 consequence?

A

Loss of PHD activity and excessive angiogenesis as VHL cannot bind to H-IFa, thus HIF not degenerated.

Brain haemangiomas.

209
Q

In reversible competitive enzyme inhibition, what happens to Vmax and KM?

A

Vmax does not change

KM increases as more substrate needed to fight for site (right shift in LB plot)

210
Q

40% ethanol with dialysis and ventilation is used to treat methanol poisoning - an example of competitive binding/ inhibition.
What is the KM difference in ethanol and methanol?
What does methanol poisoning result in? (2)

A

Alcohol dehydrogenase KM for ethanol is higher than methanol.

Results in blindness from formaldehyde and metabolic acidosis.

211
Q

What is the difference between orthostatic and allosteric site?

A

Orthostatic site - same site

Allosteric site - different site

212
Q

Treatment for methanol poisoning (3)

A

40% ethanol with dialysis and ventilation

213
Q

In reversible non-competitive enzyme inhibition, what happens to Vmax and KM?

A 
Vmax reduced (Upward shift in LB plot)
KM unchanged
214
Q

What does irreversibly non-competitive enzyme inhibition involve?

A

Formation/ breakage of covalent bond in enzyme complex

215
Q

What are rate-limiting enzymes inhibited by?

Is this orthostatic or allosteric?

A

End product via negative feedback

Allosteric control

216
Q

Do allosteric enzymes follow Michaelis-Menten?

What do they exhibit?

A

No, it is a SIGMOIDAL curve instead of a hyperbola.

Exhibits cooperative binding.

217
Q

What are allosteric enzymes controlled by?

What behaviour do allosteric enzymes exhibit?

A

Activator (upward shift) and Inhibitor (downward shift)

Co-operative behaviour

218
Q

What is cooperativity?

1 Example of positive co-operativity?

A

Effects seen only AFTER substrate has bound where affinity increases
*Enzyme must be able to bind to >1 substrate sequentially

E.g. Hb: Hb(O2)4

219
Q

What are the negative allosteric controls of Hb?

A 
CO2
Acidosis
DPG (or 2,3-BPG)
Exercise
Temperature

**CADET shifts graph to the right (for the same PO2 there is lower O2 sat%)

220
Q

1 example of an enzyme exhibiting non-cooperative binding?

A

Myoglobin - binds to O2 tightly (MbO2)

*Follows Michaelis menten equation (hyperbolic)

Principles (14 decks)

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