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Medicine Year 1 > Principles Biochemistry > Flashcards

Principles Biochemistry Flashcards

1
Q

What is rRNA?

A

Ribosomal RNA.

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2
Q

What is the function of rRNA?

A

rRNA combines with proteins to form ribosomes, where protein synthesis takes place.

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3
Q

Define a redox reaction

A

A redox reaction is the transfer of electrons from one molecule to another.

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4
Q

Define an oxidation reaction.

A

An oxidation reaction results in the loss of electrons.

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5
Q

Define a reduction reaction.

A

A reduction reaction results in the gain of electrons.

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6
Q

Name 3 major classes of molecules.

A
  1. Peptides
  2. Proteins
  3. Lipids.
  4. Nucleic acids.
  5. Carbohydrates.
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7
Q

Give a function of a biomolecule.

A
  1. DNA
  2. Structural (bones, teeth, cartilage).
  3. Recognition/communication/specificity as hormones/receptors/enzymes.
  4. Energy currency/storage as ATP.
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8
Q

Give an example of a carbohydrate.

A

Monosaccharide, disaccharide, polysaccharide (cellulose and glycogen).

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9
Q

What is the First law of thermodynamics?

A

Energy is neither created nor destroyed.

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10
Q

What is the Second Law of thermodynamics?

A

As energy is converted from one form to another, some of the energy becomes unavailable to do work.

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11
Q

How may the free energy change (ΔG) be calculated?

A

Energy of products - energy of reactants.

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12
Q

Describe an exergonic reaction.

A

An exergonic reaction is one in which the total free energy of the products is less than that of the reactants. ΔG is NEGATIVE.

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13
Q

Can an exergonic reaction occur spontaneously or not?

A

Yes. Exergonic reactions may occur spontaneously.

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14
Q

Describe an endergonic reaction.

A

Reactions in which the total free energy of the products is greater than that of the reactants. ΔG is POSITIVE.

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15
Q

Can an endergonic reaction occur spontaneously?

A

No. they require an input of energy in order to proceed.

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16
Q

ΔG values near zero are characteristic of which type of reaction?

A

Readily reversible reactions.

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17
Q

What does ΔG = 0 indicate about the system?

A

It indicated the system is at equilibrium.

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18
Q

Phosphoglucomutase catalyses which reaction?

A

Glucose-6-phosphate Glucose-1-phosphate.

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19
Q

Glucose-6-phosphate Glucose-1-phosphate.

What are the forward and backward reactions involved in?

A

Forward: glycogen synthesis.
Backward: glycogen breakdown.

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20
Q

How may unfavourable cellular processes be driven?

A

By coupling them to highly favourable processes.

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21
Q

What is ATP used for?

A

It is a universal energy currency for driving many different cellular processes.

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22
Q

Is ATP stored in cells in large amounts?

A

No, it is constantly regenerated.

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23
Q

How may ATP be regenerated?

A

Using creatine phosphate.

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24
Q

What type of energy bonds do anhydride bonds possess?

A

High energy bonds.

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25
Q

Define metabolism.

A

The sum of all the reactions taking place in the body.

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26
Q

What 2 things can metabolism be divided into?

A

Catabolism and anabolism.

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27
Q

Define catabolism.

A

The breakdown of molecules (releases energy).

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28
Q

Define anabolism.

A

The synthesis of molecules (consumes energy).

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29
Q

Give a brief definition of glycolysis

A

The initial breakdown of glucose for the generation of ATP.

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30
Q

What is the net gain of ATP per glucose molecule?

A

net gain of 2 ATP. (2 ATP are initially used, and later steps generate 4 ATP - net gain of 2 ATP).

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31
Q

Define gluconeogenesis.

A

Production of glucose from non-carbohydrate precursors, e.g. pyruvate.

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32
Q

Does gluconeogenesis produce or consume energy?

A

It consumes energy.

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33
Q

Is gluconeogenesis the reverse of glycolysis?

A

No.

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34
Q

What significance do reactions with largely negative ΔG values have in metabolic pathways?

A

They serve as useful control points.

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35
Q

How is flux through control points in metabolic pathways controlled?

A

By altering enzyme activity.

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36
Q

Describe a water molecule.

A

Polar molecule whose electrons are unequally shared.

It is bent, forming a dipole with a tetrahedral shape.

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37
Q

Describe a hydrogen bond.

A

A polarised covalent bond existing between hydrogen and a more electronegative atom. Individually weaker than covalent bonds. Often linear.

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38
Q

What is an amphipathic (amphiphilic) molecule?

A

One which is both hydrophilic and hydrophobic.

It has a polar hydrophilic head (choline, carboxylic acid) and non-polar hydrophobic tail (hydrocarbon).

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39
Q

What do amphipathic molecules form when in water?

A

Micelles.

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40
Q

Describe a peptide bond..

A

They have partial double bond character.

They are planar, strong and rigid.

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41
Q

What is an acid?

A

A molecule capable of donating a proton.

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42
Q

What is a base?

A

A molecule capable of accepting a proton.

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43
Q

What is strength a measure of (in terms of acids and bases)?

A

Strength of an acid is how readily the substance can donate a proton.

Strength of a base is how readily the substance can accept a proton.

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44
Q

What is the pH of a solution?

A

A measurement of the number of protons within the solution.

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45
Q

What is a buffer?

A

A solution controlling the pH of a reaction mixture.

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46
Q

What special property do buffers have that makes them useful?

A

At their pKa, buffers resist a change of pH on addition of moderate amounts of acid or base.

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47
Q

Are proteins capable of acting as buffers? Explain.

A

Yes, pH changes can change the ionisation of a protein, leading to structural and functional changes.

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48
Q

What is a primary protein structure?

A

A sequence of amino acid residues.

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49
Q

What is a secondary protein structure?

A

A localised confirmation of a polypeptide backbone.

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50
Q

Give an example of a secondary protein structure.

A
  1. Alpha helix
  2. beta strands and sheets
  3. Triple helix
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51
Q

What may break an α helix?

A

Proline residues.

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52
Q

what is an α helix an example of?

A

A secondary protein structure.

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53
Q

Give an example of a triple helix.

A

Collagen.

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54
Q

What is a tertiary protein structure?

A

A 3D structure of an entire polypeptide, including all its side chains.

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55
Q

What is a quarternary protein structure?

A

Arrangement of multiple polypeptide chains in a protein with many (non-/identical) subunits.

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56
Q

Polypeptides can rotate around angles between what?

A
  1. α carbon and amino group.

2. α carbon and carboxyl group.

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57
Q

Sickle cell anaemia is the result of what?

A

A single nucleotide sequence change resulting in an altered protein (valine instead of glutamic acid).

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58
Q

Incorrectly folded proteins may associate with other proteins to cause which conditions?

A

Alzheimer’s and Parkinson’s etc.

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59
Q

Protein structure may be denatured by what? Give two examples.

A
  1. heat
  2. Extreme pH
  3. Detergents
  4. Urea
  5. Guanine hydrochloride
  6. Thiol agents
  7. Reducing agents.
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60
Q

What is the genome?

A

The total DNA in each cell (the genetic information of the organism).

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61
Q

DNA nucleotide sequences determine what?

A

Amino acid sequences of polypeptide chains.

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62
Q

What is transcription?

A

DNA nucleotides are transcribed to RNA nucleotides.

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63
Q

What is translation?

A

RNA nucleotides are translated to amino acids to form proteins.

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64
Q

What is a nucleoside?

A

A base + a sugar.

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65
Q

What is a nucleotide?

A

A nucleoside + a phosphate group.

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66
Q

What is polymerisation?

A

The formation of a phosphodiester bond between a free 3’ OH group and a 5’ triophosphate.

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67
Q

Nucleotides are added to which end of the DNA strand.

A

3’ ONLY.

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68
Q

DNA exists as what?

A

A double helix of base pairs. Two anti-parallel nucleotide strands (5’ to 3’ and 3’ to 5’).

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69
Q

What bond exists between adenine and thymine?

A

double bond.

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70
Q

what bond exists between cytosine and guanine?

A

Triple bond.

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71
Q

DNA replication is catalysed by what?

A

DNA polymerase.

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72
Q

What is required to start DNA replication?

A

An RNA primer.

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73
Q

Where does replication begin within the genome?

A

At several points simultaneously to ensure the process is reasonably quick.

74
Q

What does semi-conservative DNA replication mean?

A

Both copies of DNA contain one original strand and one new strand.

75
Q

Is DNA replication uni- or bi-directional?

A

Bidirectional, ensures quick replication.

76
Q

Which is the leading and lagging strand in DNA replication?

A

Leading: 3’ to 5’.
Lagging: 5’ to 3’ and produces Okazaki fragments.

77
Q

What is the role of helicase in DNA replication?

A

Helicase unwinds DNA and prevents it from rewinding.

78
Q

What does primate synthesise?

A

An RNA primer.

79
Q

What does DNA polymerase synthesise?

A

A complementary DNA strand.

80
Q

What happens at the end of DNA replication?

A

RNA primers are degrade and DNA polymerase fills in any gaps.

81
Q

What are the 3 main classes of RNA?

A
  1. Ribsomal.
  2. Transfer.
  3. Messenger.
82
Q

What is the function of ribsomal RNA (rRNA)?

A

rRNA combines with proteins to form ribosomes, where protein synthesis takes place.

83
Q

What is the function of transfer RNA (tRNA)?

A

tRNA carries amino acids, enabling them to be incorporated into proteins. They are adapters between nucleic acid and amino acid codes.

84
Q

What is the function of messenger RNA (mRNA)?

A

mRNA carries genetic information for protein synthesis, i.e. codes for the synthesis of proteins.

85
Q

How do RNA and DNA bases differ?

A

RNA contains uracil instead of thymine.

86
Q

rRNA makes up what percentage of the total cellular RNA?

A

60%.

87
Q

tRNA makes up what percentage of the total cellular RNA?

A

15%

88
Q

mRNA makes up what percentage of the total cellular RNA?

A

5%

89
Q

Anti-codon consists of how many nucleotides?

A

3

90
Q

How is RNA made?

A

By RNA polymerases. One DNA strand is used as a template to copy the nucleotide sequence into RNA.

91
Q

Eukaryotic cells have three types of RNA polymerase which are?

A

Pol I, Pol II, Pol III.

92
Q

Pol II is responsible for synthesising what?

A

mRNA

93
Q

What are the stages of transcription?

A
  1. RNA polymerase binding.
  2. DNA chain separation.
  3. Transcription initiation.
  4. Elongation.
  5. Termination.
94
Q

What does TBP stand for? What is its function?

A

TATA-box Binding Protein. It recognises the TATA box and introduces kink into DNA, determines transcriptional start and direction.

95
Q

Which direction is RNA synthesised? What is its relationship to the template strand.

A

5’ to 3’. The new RNA sequence is complementary to the template strand and identical to the coding strand.

96
Q

What is the function of an enhancer?

A

It binds to specific DNA sequences in the vicinity of a promoter to regulate transcription.

97
Q

Coordinated gene expression may occur in response to what?

A

Specific stimuli, e.g. hormones, cellular stress.

98
Q

Where are steroid receptors located when they are inactive?

A

In the cell cytoplasm.

99
Q

How do steroid receptors become active and where are they then located?

A

By binding a ligand (steroid), they move to the cell nucleus and bind to DNA at steroid-response elements (SREs).

100
Q

How are steroids transported?

A

Steroids are transported in the blood bound to albumin or specific transport proteins.

101
Q

How do free steroids enter target cells?

A

By diffusion, they then bind to inactive steroid receptors in the cytoplasm, which then translocates to the nucleus.

102
Q

What are exons?

A

Regions that code for DNA.

103
Q

What are introns?

A

Regions that do not code for DNA.

104
Q

What happens during translation with regards to codon-anticodon base pairing?

A

Anti-codons of tRNA molecules form base pairs with codons on mRNA.

105
Q

What are the energy sources of translation?

A

ATP and GTP.

106
Q

What binds amino acids to their corresponding tRNA molecules?

A

Aminoacyl-tRNA synthesases.

107
Q

What size is a eukaryotic ribosome?

A

80S.

108
Q

Ribosomes have 3 tRNA binding sites, name them.

A
  1. Exit.
  2. Peptidyl.
  3. Aminoacyl.
109
Q

What catalyses peptide bond formation between amino acids at the Peptidyl and Aminoacyl sites?

A

Peptidyl transferase.

110
Q

What moves ribosomes along mRNA?

A

Elongation factor (EF-2).

111
Q

When does termination occur?

A

When the aminoacyl site of a ribosome encounters a stop codon.

112
Q

What is a point mutation?

A

A change in a single DNA base.

113
Q

What is a missense mutation?

A

Results in a change of amino acid sequence, and may change protein function e.g. sickle cell anaemia.

114
Q

What is a nonsense mutation?

A

Creates a new termination codon, changing the length of the protein due to a premature stop of translation.

115
Q

What is a silent mutation?

A

No change in amino acid sequence, is due to degeneracy of the genetic code and has no effect on protein function.

116
Q

What is a frameshift mutation?

A

The addition or deletion of a single base (or two) which changes how the DNA sequence is read.

117
Q

Give examples of chromosomal mutations.

A

Deletions, duplications, inversions and translocations.

118
Q

What happens to finished proteins?

A
  1. Targeting (moves to final cellular destination).
  2. Modification (addition of chemical groups).
  3. Degradation (unwanted or damaged proteins are removed).
119
Q

Where are proteins produced by free ribosomes in the cytosol destined for?

A
  1. cytosol
  2. nucleus
  3. mitochondria
  4. translocated post-translationally.
120
Q

Where are proteins produced on the rough endoplasmic reticulum destined for?

A
  1. Plasma membrane
  2. Endoplasmic reticulum
  3. Golgi apparatus
  4. Secretion
  5. Translocated co-translationally.
121
Q

Define glycosylation.

A

The addition and processing of carbohydrates in the ER and Golgi.

122
Q

The hereditary form of emphysema results from what?

A

The misfolding of the protein α1-antitrypsin in the ER.

123
Q

What is the function of an enzyme?

A

Speeds up the rate at which a reaction reaches equilibrium.

124
Q

Describe the action of an enzyme.

A

They bind and stabilise the transition state, i.e. the reaction intermediate species that has the greatest free energy. They reduce the activation energy by providing alternative reaction pathways.

125
Q

What is glycogen storage disease?

A

An enzyme deficiency that results in failure of glycogen to enter the transition phosphorylated state. Causes defective glycogen synthesis/breakdown in muscle, liver and kidney.

126
Q

Symptoms of glycogen storage disease?

A

hypoglycaemia, hepatomegaly, skin and mouth ulcers, bacterial and fungal infection, bowel inflammation and irritability.

127
Q

What properties do cofactors/coenzymes offer to many enzymes?

A

Catalytic activity.

128
Q

How are cofactors and coenzymes differentiated?

A

Cofactors are made of metal ions and are inorganic.

Coenzymes are organic molecules.

129
Q

What are isozymes?

A

Isoforms of enzymes that catalyse the same reaction, but have different properties, structure and sequence.

130
Q

How does lactate dehydrogenase (example of an isozyme) function differ in the heart and in muscle?

A

In the heart it promotes aerobic metabolism.

In muscle it promotes anaerobic metabolism.

131
Q

What is Creatine kinase?

A

A dimeric protein which binds to muscle sarcomere.

132
Q

Creatine kinase of brain type BB, suggests what?

A

Stroke or tumour.

133
Q

Creatine kinase of heart type MB, suggests what?

A

Heart attack.

134
Q

What are phosphorylation reactions carried out by?

A

Protein kinases.

135
Q

What are zymogens?

A

Inactive precursors of an enzyme, e.g. trypsinogen and chymotrypsinogen.

136
Q

What is an apoenzyme?

A

An enzyme without a cofactor.

137
Q

What is a prosthetic group?

A

Tightly bound coenzymes, e.g. haem in haemoglobin.

138
Q

What is a holoenzyme?

A

An enzyme with a cofactor.

139
Q

What is Vmax?

A

The maximum velocity of a reaction.

140
Q

What is Km?

A

The concentration in moles of S which gives 1/2 Vmax.

Km = [S] at 0.5Vmax.

141
Q

What does a low Km indicate?

A

A low Km indicates an enzyme only needs a little substrate to work at half-maximal velocity.

142
Q

What does a high Km indicate?

A

A high Km indicates an enzyme needs a lot of substrate to work at half-maximal velocity.

143
Q

What do proline hydroxylates enable?

A

Proline hydroxylases enable sensing of physiological oxygen ranges.

144
Q

Define competitive inhibition.

A

an inhibitor binds to the active site, blocking substrate access.

145
Q

What is orthosteric inhibition?

A

Competitive inhibition, binds at the same site.

146
Q

What is non-competitive inhibition?

A

An inhibitor binds to a site other than the active site, inhibiting an enzyme by changing its conformation.

147
Q

What is allosteric inhibition?

A

Non-competitive inhibition, binds at different sites.

148
Q

What is irreversible inhibition?

A

Non-competitive inhibition which cannot be reversed. It usually involves formation or breakage of covalent bonds in the enzyme complex.

149
Q

What effect does competitive inhibition have on Vmax and Km?

A

Vmax does not change, but Km varies.

150
Q

How is methanol poisoning treated?

A

With 40% ethanol + dialysis + ventilation.

151
Q

What effect does non-competitive inhibition have on Vmax and Km?

A

Vmax varies, but Km does not change.

152
Q

What type of curve do allosteric enzymes produce?

A

Sigmoidal.

153
Q

What is V0?

A

The initial reaction velocity.

154
Q

Glucose may be converted into what?

A
  1. Storage: glycogen, starch, sucrose, conversion to lipid.
  2. Ribose-5-phosphate.
  3. Lactate.
  4. Pyruvate.
155
Q

What is ribose-5-phosphate used for?

A

It is a precursor for nucleotide synthesis and DNA repair. It is essential for growth..

156
Q

Why is lactate important in anaerobic glycolysis?

A

It enables the rapid, but inefficient production of ATP in the absence of oxygen.

157
Q

What is pyruvate used for?

A

Efficient ATP production by oxidative metabolism.

158
Q

Which glucose symporters allow glucose transport into the brain?

A

GLUT1 and GLUT 3.

159
Q

Which glucose symporters allow glucose transport into the Liver?

A

GLUT2

160
Q

Which glucose symporters allow glucose transport into muscle and adipose tissue?

A

GLUT4

161
Q

Which glucose symporters allow glucose transport into the gut?

A

GLUT5

162
Q

What are the 3 control points in glycolysis?

A
  1. Hexokinase: controls substrate energy.
  2. Phosphofructokinase: controls the rate of flow.
  3. Pyruvate kinase: controls product exit.
163
Q

What effect does AMP have on glycolysis?

A

Will increase rate of glycolysis if energy is needed.

164
Q

What effect does ATP have on glycolysis?

A

Will slow glycolysis if energy is abundant.

165
Q

What effect does citrate have on glycolysis?

A

Slows pyruvate entry to TCA cycle if energy is abundant.

166
Q

What effect does H+ have on glycolysis?

A

Slows glycolysis if there is too much lactic acid being produced.

167
Q

What is the pyruvate produced in glycolysis used for?

A

Carbon to fuel the TCA cycle in mitochondria.

168
Q

What is the NADH produced in glycolysis used for?

A

For the electron transport chain and ATP synthesis.

169
Q

What happens if mitochondrial metabolism is inhibited by lack of oxygen?

A

NADH is used to ferment pyruvate to lactic acid (lactate).

NADH is then regenerated.

170
Q

What is the Warburg effect?

A

The up-regulation of anaerobic glycolysis in cancer cells.

171
Q

How do cancer cells produce energy?

A

By high-rate of glucose metabolism to lactate, i.e. anaerobic glycolysis.

172
Q

Why is NADH reoxidised?

A

To enable glycolysis to continue.

173
Q

How is NAD+ regenerated and why?

A

Through the oxidative metabolism of pyruvate. Acts as an electron acceptor to maintain Stage 1 and 2 metabolism.

174
Q

Stage 2 of aerobic respiration has 3 different names, what are these?

A
  1. Citric acid cycle.
  2. Krebs cycle
  3. Tricarboxylic acid cycle.
175
Q

Where does the TCA cycle occur?

A

In mitochondria.

176
Q

Where are the enzymes for the TCA cycle contained?

A

The matrix of the mitochondria.

177
Q

How can pyruvate enter the mitochondrial matrix?

A
  1. H+ gradient from the cytosol to the matrix.
  2. Pyruvate transporter by facilitated diffusion.
    3.
178
Q

When in the mitochondrial matrix, how is pyruvate metabolised to Acetyl-CoA?

A

Pyruvate dehydrogenase complex catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA.

179
Q

Can acetyl-CoA be converted back to pyruvate?

A

No, the reaction is irreversible.

180
Q

Summarise the TCA cycle.

A

2C unit from acetyl-CoA condense with a 4C unit to form 6C unit.

Medicine Year 1 (1 decks)

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