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Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

van der Waals Interactions

A

interactions of electrons of non polar substances

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2
Q

what is electronegativity?

A

the attractive force that an atomic nucleus exerts on electrons within a bond

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3
Q

what is acylation?

A

the addition of an acyl group -C(O)-R

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4
Q

what is a carboxyl group

A

COOH

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5
Q

esterification

A

carboxyl group and alcohol group makes an ester link plus water

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6
Q

what happens during redox reactions

A

electrons are transferred from one molecule to another

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7
Q

what are the four major classes of biomolecules?

A

peptides and proteins (consist of amino acids), lipids (triglycerides, phospholipids, steroids), nucleic acids (DNA, RNA) and carbohydrates

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8
Q

different types of carbohydrates

A

mono, di and polysaccharides

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9
Q

different types of lipids

A

triglycerides, phospholipids and steroids

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10
Q

what is a nucleoside?

A

base + sugar

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11
Q

what is a nucleotide?

A

base + sugar (nucleoside) + phosphate group

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12
Q

what is a phosphodiester bond formed between?

A

a free 3’ OH group and a 5’ triphosphate (nucleotide)

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13
Q

what enzyme adds the next deoxyribonucleotide to the -OH group at the 3’ end of the growing strand?

A

DNA polymerase

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14
Q

what happens to the pyrophosphate ion when the nucleotide attaches to the growing strand?

A

it is broken apart, releasing energy to drive the reaction

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15
Q

what end are nucleotides added to?

A

only added to a free 3’end

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16
Q

what is the bond called that links the DNA chain together? They are between 3’ OH group and 5’ triphosphate

A

phosphodiester

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17
Q

what bonding to base pairs take part in?

A

hydrogen bonding from one strand to the other

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18
Q

when does DNA have to be replicated?

A

before cell division

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19
Q

why does DNA have to be replicated?

A

to ensure the daughter cells have a full complement of the genome

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20
Q

what catalyses DNA replication?

A

DNA polymerase

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21
Q

what does DNA need to start replication?

A

an RNA primer

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22
Q

what is the name of the strand that has to add nucleotides in fragments?

A

the lagging strand

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23
Q

what are the fragments of nucleotides called that are added to the lagging strand?

A

OKAZAKI fragments

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24
Q

what enzyme unwinds DNA?

A

helicase

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25
Q

the enzyme that synthesises a complementary DNA strand

A

DNA polymerase

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26
Q

what synthesises an RNA primer?

A

primase

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27
Q

what does rRNA do?

A

combines with proteins to form ribosomes where protein synthesis takes place

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28
Q

tRNA does what?

A

carries the amino acids to be incorporated into the protein

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29
Q

mRNA does what?

A

carrier the genetic information for protein synthesis

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30
Q

how many types of RNA polymerase do prokaryotic cells have?

A

one type of RNA polymerase

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31
Q

what does Pol 2 RNA polymerase synthesise?

A

all mRNA

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32
Q

where is the TATA box present?

A

about 25 nucleotides before the transcriptional start (-25)

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33
Q

what recognises the TATA box?

A

TATA box binding protein (TBP)

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34
Q

What does the TBP do?

A

It introduces kink into DNA

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35
Q

what does the TBP provide?

A

a landing platform for further transcription factors and for RNA polymerase

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36
Q

what does the initiation of transcription require?

A

additional general transcription factors

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37
Q

what direction is the RNA chain synthesised in?

A

5’ to 3’ direction

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38
Q

what is the new RNA sequence identical to?

A

the coding strand (but uracil instead of T)

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39
Q

what structure does RNA make?

A

stem-loop structure followed by a stretch of Us

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40
Q

what type of specific transcription factors are required?

A

DNA-binding domain and transcriptional activation domain

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41
Q

what are enhancers and how do they specifically regulate transcription?

A

an enhancer is a short (50–1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. They are specific transcription factors

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42
Q

what happens to the primary mRNA once it has been spliced?

A

a 5’ G cap and a poly(A) tail is added

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43
Q

do tRNA molecules have codons or anticodons?

A

anticodons

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44
Q

what do the anticodons on tRNA do?

A

form base pairs with the codons on mRNA

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45
Q

the genetic code is generate- meaning?

A

many amino acids have more than one codon

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46
Q

the genetic code is unambiguous meaning?

A

each codons codes for only one amino acid or a stop

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47
Q

what 7 components are needed for translation?

A
  • amino acids
  • tRNA
  • aminoacyl-tRNA synthetases
  • a specific set of protein factors for the initiation of protein synthesis, the elongation of polypeptide chain and translocation and termination
  • ATP and GTP as energy sources
  • ribosomes
  • mRNA
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48
Q

what are aminoacyl-tRNA synthetases?

A

they bind amino acids to their corresponding tRNA molecule and are highly specific. There is at least one for every amino acid

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49
Q

how many rRNA molecules are in ribosomes?

A

four

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50
Q

what are the three tRNA binding sites on ribosomes?

A

Exit, peptidyl and aminoacyl

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51
Q

what does initiation require?

A

initiation factors?

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52
Q

what provides energy for initiation?

A

hydrolysed GTP

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53
Q

what brings the next aminocyl-tRNA to the A site (aminoacyl site)?

A

an elongation factor

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54
Q

when does termination occur?

A

when the A site of the ribosome encounters a stop codon

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55
Q

what are the three stop codons?

A

UAA, UAG or UGA

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56
Q

what binds to a stop codon?

A

a release factor

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57
Q

point mutation

A

change in a single base in DNA (there are different types of point mutations)

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58
Q

missense mutation

A

one base is changed which produces a different amino acid sequence which can alter proteins function

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59
Q

nonsense mutation

A

base change creates a stop codon. shortens length of amino acid chain

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60
Q

silent mutation

A

base change which doesn’t alter the amino acid

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61
Q

frameshift mutation

A

addition or deletion of a single base which changes the reading frame of translation into protein

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62
Q

four types of chromosomal mutations

A

deletions, duplications, inversions and translocations

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63
Q

what is targeting?

A

moving a protein to its final cellular destination

64
Q

what three things happen to the finished protein?

A

targeting, modifications and degradation

65
Q

bound ribosomes on the rough endoplasmic reticulum make proteins destined for… (4)

A
  • plasma membrane
  • ER
  • Golgi apparatus
  • secretion
66
Q

how are proteins that are made on the rough endoplasmic reticulum translocated?

A

they are translocated co-translationally

67
Q

post-translational modification: glycosylation

A

addition and processing of carbohydrates in the ER and the Golgi

68
Q

post-translational modification in the ER

A

formation of disulphide bond and folding of multisubunit proteins

69
Q

what model is used to explain the relationship between Vmax and Km?

A

The Michaelis-Menten model

70
Q

how are Vmax and Km measured?

A

measure the initial reaction velocity, V0, at a known substrate concentration and repeat at increasing substrate concentration

71
Q

what is the Michaelis Constant (Km) equivalent to?

A

The substrate concentration where the initial reaction rate is half of the Vmax

72
Q

What graph enables accurate determination of Vmax and Km?

A

The Lineweaver-Burk plot

73
Q

instead of V against [S], you plot…

A

1/V over 1/[S]

74
Q

where can you read the V max on a Lineweaver Burk plot?

A

intersection of the straight line on the y axis

75
Q

where can you read the Km on a Lineweaver Burk plot?

A

on the intersection with the X axis

76
Q

what is the Vmax

A

the maximum rate of reaction at unlimited substrate concentration (point at which the line crosses the Y axis)

77
Q

what is the Km?

A

substrate concentration that gives half Vmax also known as Michaelis Constant (point at which the line crosses the X axis)

78
Q

what does a low Km mean?

A

an enzyme only needs a little substrate to work at half-maximal velocity

79
Q

what does a high Km mean?

A

an enzyme needs a lot of substrate to work at half-maximal velocity

80
Q

what is glucokinase?

A

a gene that helps the body to recognise how high the blood glucose level is in the body

81
Q

opposite to allosteric inhibition

A

orthosteric inhibition. the inhibitor binds to the same active site

82
Q

effects of competitive inhibition of Vmax and Km?

A

Vmax does not change but the Km does

83
Q

effects of non- competitive inhibition of Vmax and Km?

A

Vmax does change but the Km does not

84
Q

common mechanism of allosteric control ?

A

feedback inhibition

85
Q

what are allosteric enzymes?

A

enzymes that change their conformational ensemble upon binding of an effector

86
Q

what is an allosteric site?

A

places on the enzyme where any enzyme regulator can bind

87
Q

what can control allosteric enzymes?

A

allosteric inhibitors and allosteric activators

88
Q

how do enzymes reduce the activation energy>?

A

provide alternative pathways

89
Q

what are cofactors?

A

molecules that enzymes depend on for catalytic activity. Metal ions (zinc, iron, copper) and they stabilise transition states. In the centre

90
Q

what are coenzymes?

A

molecules that enzymes depend on for catalytic activity and are usually organic molecules.

91
Q

what are tightly bound coenzymes called?

A

prosthetic groups

92
Q

where are many coenzymes deprived from?

A

vitamins

93
Q

What are coenzymes involved in?

A

redox reactions and group transfer processes (ATP transfers phosphate groups)

94
Q

what are the amino acids on an active sites essential for?

A

for catalytic activity and highly specific interactions

95
Q

what is an isoform?

A

any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence

96
Q

what are isozymes?

A

isoforms of enzymes. Enzymes with different properties, structure and sequence but are able to catalyse the same reaction

97
Q

how can enzymes have covalent modification?

A

side groups of serine, threonine and tyrosine can form phosphate esters

98
Q

how can enzymes be activated or deactivated?

A

phosphorylation or dephosphorylation

99
Q

what carries out phosphorylation?

A

protein kinases

100
Q

what carries out dephosphorylation?

A

protein phosphatase

101
Q

what are zymogens?

A

inactive precursors of an enzyme that are irreversibly transformed into active enzymes by cleavage of a covalent bond

102
Q

examples of zymogens?

A

digestive enzymes, blood-clotting enzymes, clot-dissolving enzymes

103
Q

what is an enzyme without a cofactor called?

A

apoenzyme

104
Q

what is an enzyme with a cofactor called?

A

holoenzyme

105
Q

how can you create a holoenzyme?

A

apoenzyme + cofactor

106
Q

difference between anabolism and catabolism

A
  • in anabolism, the complexity increases but in catabolism the complex is broken down into more simple molecules
  • anabolism requires energy and catabolism yields energy
107
Q

anabolism is e……gonic and ……

A

endogonic and reductive

108
Q

catabolism is e…….gonic and …….

A

exogonic and oxidative

109
Q

examples of oxidised precursors in metabolism

A

CO2 and H2O

110
Q

basic structure of glycogen

A

A glucose chain

111
Q

examples of cells that only use glucose as an energy source

A

erythrocytes, retina, renal medulla (in the kidney), all cancer cells, brain

112
Q

basic structure of disaccharides

A

a double sugar formed with two monosaccharides or simple sugars

113
Q

how is glucose transported into cells?

A

via Na+/glucose symporters and via passive facilitated diffusion glucose transporters

114
Q

what are the three ‘control point’ enzymes?

A

hexokinase (substrate entry), phosphofructokinase (rate of flow) and pyruvate kinase (product exit)

115
Q

what are two activators that will increase glycolysis if energy is needed?

A

AMP and fructose 2,6-biphosphate

116
Q

what are two inhibitors that will inhibit the act of phosphofructokinase?

A

ATP, Citrate and H+ ions

117
Q

effect of too much ATP on glycolysis?

A

glycolysis will show down

118
Q

what is citrate?

A

a citric acid cycle intermediate

119
Q

effect of H ion inhibition on phosphofructokinase?

A

slows down glycolysis if too much lactic acid is being produced

120
Q

another name for the ATP/AMP ratio?

A

the energy charge

121
Q

what is the Warburg effect?

A

the up-regulation of anaerobic glycolysis in cancer cells to produce lactate

122
Q

3 drugs that can target glycolysis and treat cancer?

A

2-deoxy-glucose, 3-bromopyruvate and dichloroacetate

123
Q

what shape will the graph of allosteric controlling enzymes have? (regulation of haemoglobin)

A

Sigmoid

124
Q

what shape will the graph of myoglobin show?

A

Hyperbolic (Michaelis menten regulation)

125
Q

where is cholesterol present and what is it a precursor of?

A

present in: cell membranes, component of myelin sheath

Precursor for: steroid hormones, vitamin D and bile acids

126
Q

what does the leading strand of DNA replication always have?

A

A free 3’ end (where nucleotides are added)

127
Q

what are the types of eukaryotic RNA polymerase?

A

Pol 1, 2, 3

128
Q

what is FF2D?

A

a general transcription factor required for all Pol 2 transcribed genes

129
Q

what is the start codon in translation?

A

AUG

130
Q

five steps of transcription

A
  1. RNA polymerase binding
  2. DNA chain separation
  3. Transcription initiation
  4. Elongation
  5. Termination
131
Q

four steps of translation

A
  1. Initiation
  2. Elongation
  3. Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites
  4. Termination
132
Q

what triggers the termination of translation?

A

When the A site of the ribosome encounters a stop codon (UAA, UAG, UGA)

133
Q

what does the description ‘degenerate’ mean in relation to the genetic code?

A

many amino acids have more than one codon

134
Q

what does unambiguous mean in relation to the genetic code?

A

each codon only codes for one amino acid

135
Q

what is the initial pathway fr the conversion of glucose to pyruvate?

A

glycolysis

136
Q

what is the net gain of ATP for one glucose molecule in glycolysis?

A

4 ATP

137
Q

what enzymes phosphorylates glucose in glycolysis to glucose-6-phosphate?

A

hexokinase

138
Q

role of phosphofructokinase in glycolysis?

A

it phosphorylates fructose-6-phosphate to fructose-1,6-biphosphate

139
Q

what is the key enzyme in the control of glycolysis?

A

Phosphofuctokinase

140
Q

negative modulators of phosphofructokinase?

A

ATP, citrate, H+

decrease glycolysis when energy is abundant

141
Q

positive modulators of phosphofructokinase?

A

AMP, fructose, 2,6-biphosphate

increase glycolysis when energy is required

142
Q

fate of pyruvate in anaerobic conditions

A

alcoholic fermentation, lactic acid formation

143
Q

describe the structure of mitochondria

A

has an inner membrane (proteins), an outer membrane and a central matrix which contains enzymes of the TCA cycle AND CRISTAE folds

144
Q

what is used to ferment pyruvate to lactic acid?

A

NADH

145
Q

where does the oxidative metabolism of pyruvate occur?

A

in the mitochondria

146
Q

describe the Krebs cycle?

A

2-carbon unit from acetyl CoA (from pyruvate) combines with a 4-carbon unit to form a 6 carbon unit
6C is decarboxylated twice so 2x CO2 are released, recreating a 4 carbon unit

147
Q

total products of two cycles of the Krebs cycle|?

from 2 acetyl-coA

A

4 CO2
2 ATP
2 FADH2
6 NADH + H+

148
Q

what is the one enzyme of the TCA cycle not located in the central matrix of the mitochondrion ?

A

succinate dehydrogenase (it’s in the inner mitochondrial membrane)

149
Q

what is phosphoryl transfer potential?

A

free energy change for ATP hydrolysis

150
Q

what is the electron transfer potential?

A

aka the redox potential of a compound

How readily a substance donates electrons

151
Q

what does a negative redox potential mean?

A

the reduced form of X has lower affinity for electrons than hydrogen

152
Q

what does a positive redox potential mean?

A

the reduced form of X has a higher affinity for electrons than hydrogen

153
Q

how does the transfer of electrons move through the respiratory chain?

A

coupled to H+ transport from mitochondrial matrix to inter membrane space
The flow of H+ back into the matrix, following the concentration gradient, phosphorylates ADP to ATP

154
Q

what inhibits oxidative phosphorylation?

A

cyanide, azide and CO inhibit the transfer of electrons to O2 so no proton gradient is formed, no ATP synthesised

155
Q

in oxidative phosphorylation, what is used to reduce O2 and H20?

A

Electrons from NADH and FADH2

156
Q

Total ATP yield

A
  • Glycolysis – 2 ATP
  • TCA cycle (2 GTP) – 2ATP
  • Glycolysis, PDH, TCA (10 NADH + H+) - 25 ATP
  • TCA (2 FADH2) – 3 ATP
  • 1 glucose molecule yields 30-32 ATP molecules

Principles (11 decks)

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