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Biochemistry Flashcards

1
Q

What are the four most common biochemical reactions?

A

phosphorylation
acylation
carboxylation
esterification

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2
Q

What is the most electronegative species?

A

oxygen so it is the terminal electron acceptor

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3
Q

What are the main functions of biomolecules?

A 
information storage
structure
energy generation
energy storage
recognition/ communication/ specificity
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4
Q

What are the major classes of biomolecules?

A

peptides/protreins
lipids
nucleic acids
carbohydrates

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5
Q

What is the first law of thermodynamics?

A

energy is neither created nor destroyed

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6
Q

What is the second law of thermodynamics?

A

when energy converts forms some of it becomes unavailable to do work

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7
Q

What does delta G equal?

A 
dG= dH-TdS
dG= (energy of products) - (energy of reactants)
dG= dG(standard conditions) + RTln([C][D]/[A][B])
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8
Q

What is an exergonic reaction?

A

has a negative dG so free energy of the products is less than the reactants so this will occur spontaneously

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9
Q

What is an endergonic reaction?

A

positive dG so free energy fo the products is more that the reactants so this won’t occur spontaneously

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10
Q

How are some unfavourable processes achieved?

A

they are coupled with a favourable process so they are possible together
ATP –> ADP has a very negative dG so can be coupled with an unfavourable reaction

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11
Q

Why is ATP unstable?

A

negative charges close together so must be regenerated lots tasing creatinine phoshate and ADP

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12
Q

What is catabolism?

A

breaking down larger molecules into smaller ones releasing energy

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13
Q

What is anabolism?

A

making large molecules from small ones using energy

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14
Q

What type of reactions are glycolysis and gluconeogenesis?

A

glycolysis is catabolic with a net gain of 2 ATP

gluconeogenesis is anabolic with a loss of energy

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15
Q

What type of reaction is used as a control point?

A

large dGs

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16
Q

What is the direction of a peptide?

A

N –> C bond

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17
Q

What are the majority of amino acids in our body made up of?

A

20 L amino acids with an alpha carbon

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18
Q

Why are peptide bonds partially double?

A

the lone pair on N can become a C=N

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19
Q

What is the Henderson-Hasselbalch equation?

A

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

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20
Q

What does pH equal in a buffer solution?

A

pKa

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21
Q

What is the isoelectric point?

A

the pH where a molecule has no net charge

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22
Q

What are the extra bonds in an alpha helix?

A

every 4th makes a hydrogen bond

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23
Q

What breaks alpha helices?

A

proline

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24
Q

What is the structure of a collagen triple helix?

A

three left-handed twists around each other to form one right-handed super helix
repeating structure is X-Y-Gly

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25
Q

What are the characteristics of fibrous and globular proteins?

A

fibrous are parallel across one axis so are mechanically strong
globular are folded circularly with exterior that can hydrogen bond with water but interior in hydrophobic

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26
Q

What are the factors that disrupt protein structure?

A
  • heat: vibrations
  • pH: electrostatic interactions
  • detergents, urea, guanidine hydrochloride (disrupt hydrophobic interactions)
  • Thiol agents, reducing agents (disrupt disulphide bonds)
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27
Q

What is a nucleoside?

A

base and sugar

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28
Q

What is a nucleotide?

A

nucleoside and one or more phosphate groups

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29
Q

What are the purines?

A

Adenine and Guanine

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30
Q

What are the pyrimidines?

A

Uracil, Thymine and Cytosine

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31
Q

What makes up a phosphodiester bond?

A

between 3’ OH group and 5’ triphosphate

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32
Q

What end are nucleotides added at?

A

3’

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33
Q

How many hydrogen bonds between the bases?

A

A two bonds to T

C three bonds to G

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34
Q

What is needed to start DNA replication?

A

RNA primer

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35
Q

How is DNA replication done with the two strands?

A

leading strand always has a free 3’ end

lagging strand must be replicated in Okazaki fragments

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36
Q

What makes the RNA primers that are needed for replication?

A

primase

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37
Q

What is exonuclease activity?

A

removal of the incorrect nucleotides if an error is made

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38
Q

How many types of RNA polymerase does a cell have?

A

Eukaryotic have three

Prokaryotic have one

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39
Q

What are telomeres?

A

repeat sequences of DNA that protect the chromosome ends

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40
Q

What does telomerase do?

A

extends telomeres (cancer cells reactivate this)

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41
Q

What are the main steps of transcription?

A
  • RNA polymerase binds (transcription factors needed and it detects the promoter region)
  • DNA chain separation (uses energy)
  • transcription initiation
  • elongation
  • termination
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42
Q

What is the TATA box?

A
  • promoter region that gets bound to by TBP to give a kink in the DNA which determines the direction of transcription
  • other transcription factors and RNA polymerase can bind here
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43
Q

What does newly-formed RNA look like?

A

stem-loop structure and a stretch of Us when released

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44
Q

What do enhancers do?

A

bind to DNA sequences near promoter to regulate transcription up or down

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45
Q

What is capping?

A

the process of properly ending the mRNA chains using ATP for bond formation

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46
Q

What are the three binding sites of a ribosome?

A

Exit
Peptidyl
Aminoacyl

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47
Q

What happens in initiation of translation?

A
  • GTP hydrolysed for energy

- initiator tRNA is in P site

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48
Q

What happens in elongation in translation?

A
  • next aminoacyl-tRNA to A site by elongation factor
  • GTP hydrolysed
  • second elongation factor regenerates first one to pick up next aminoacyl-tRNA
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49
Q

What happens in peptide bond formation or translation?

A
  • peptidyl transferase makes peptide bond between amino acids in P and A so peptide is formed in A site
  • elongation factors moves ribosome along
  • empty tRNA is in E, growing peptide is in P and A is free for next aminoacyl-tRNA
50
Q

What happens in termination of translation?

A

when A comes to STOP there is dissociation

51
Q

What is a point mutation?

A

a mutation in a single base

52
Q

What is a missense mutation?

A

change in amino acid sequence

53
Q

What is a nonsense mutation?

A

no change in amino acid sequence so no effect on protein

54
Q

What happens to a newly made protein?

A
  • targeted so it will move to its final destination
  • modified so more chemical groups are added
  • degraded so unwanted bits are removed
55
Q

Where do the proteins that are made by free ribosomes go to?

A

cytosol
nucleus
mitochondria
(these are moved after translation)

56
Q

Where do the proteins that are made by bound ribosomes go to?

A 
plasma membrane
ER
Golgi
secretion
(moved during translation)
57
Q

What happens to proteins after translation?

A

carbohydrates are added
disulphide bonds are formed
multisubunit proteins are formed
cleavage

58
Q

What do enzymes do to reactions?

A

stabilise the transition state
reduce activation energy
equilibrium achieved faster

59
Q

What is a glycogen storage disease?

A

enzyme deficiency that results in failure of glycogen to enter phosphorylated state eg Von Gierke’s disease

60
Q

What are cofactors?

A

metal ions that do redox reactions and stabilise transition states

61
Q

What are coenzymes?

A

organic molecules (non-protein) structure that is necessary for the functioning of an enzyme eg from vitamins, redox (NAD), CoA or ATP

62
Q

What are metalloproteins?

A

metal cofactors within an enzyme

63
Q

What are prosthetic groups?

A

tightly bound coenzymes

64
Q

What is an apoenzyme?

A

enzyme without a cofactor

65
Q

What is a holoenzyme?

A

enzyme with a cofactor

66
Q

What is made if you add a cofactor and an apoenzyme?

A

holoenzyme

67
Q

What is a cofactor necessary for?

A

the activity of an enzyme

68
Q

What is an isozyme?

A

isoforms of enzymes that catalyse the same reaction but have different properties and structure- these can be used for diagnostic purposes

69
Q

What are phosphorylation reactions?

A

carried out by protein kinases and are very fast-switch activity of the enzyme

70
Q

What are zymogens?

A

inactive precursors to enzymes that are activated by irreversible covalent modification or covalent bond cleavage

71
Q

What does Km equal?

A

(k-1 + k2)/k1

50% of Vmax is moles

72
Q

What is Vmax?

A

where the reaction velocity plateaus at a maximal rate at which the enzymes can convert substrate

73
Q

What is the Michaelis-Menten equation?

A

describes the rate of catalysis as a function of substrate concentration to give a straight line

74
Q

What does 1/V equal?

A

1/V = Km/Vmax . 1/[S] + 1/Vmax

y intercept is 1/Vmax and x intercept is -1/Km

75
Q

What does a low Km mean?

A

only a little substrate is needed for half-maximal velocity

76
Q

What does a high Km mean?

A

a lot of substrate needed to work at half-maximal velocity

77
Q

What does competitive inhibition do to Vmax and Km?

A

changes Km but not Vmax

78
Q

What does non-competitive inhibition do to Vmax and Km?

A

changes Vmax but not Km

79
Q

What do allosteric enzymes have for an M-M curve?

A

sigmoidal shape that can be controlled by allosteric inhibitors and activators

80
Q

What can you do to an endothermic reaction to make it feasible?

A

pair it with an exothermic one

81
Q

What is a largely negative deltaG reaction likely to be?

A

irreversible

82
Q

What does deltaG equal at Keq?

A

0

83
Q

What type of rotation is allowed around the nitrogen and the carbonyl group in a peptide bond?

A

single bond rotation

84
Q

Does an acid with a higher or a lower pKa dissociate more?

A

lower pKa dissociates more

higher pKa dissociates less

85
Q

What happens to pKa values with increasing acid strength?

A

become smaller

86
Q

What does collagen contain?

A

lots of hydroxylated proline residues

87
Q

What is anabolism?

A

building larger molecules using energy

88
Q

What is catabolism?

A

breaking down into smaller molecules to give out energy

89
Q

What is formed in anabolism?

A

oxidised precursor become ad reduce biosynthetic product

90
Q

What is formed in catabolism?

A

reduced fuel will become oxidised products

91
Q

What are the four ways that glucose can be transformed?

A
  • into ribose-5-phosphate by the pentose phosphate pathway
  • into pyruvate by aerobic glycolysis
  • into glycogen, starch and sucrose for storage
  • into lactate by anaerobic glycolysis
92
Q

What are the differences between each GLUT transporter?

A

they have a variable Km for glucose

93
Q

What is the equation for glycolysis?

A

glucose + 2ADP + 2Pi + 2NAD+ –> 2pyruvate + 4ATP + 2H2O + 2NADH + 2H+

94
Q

What are the intermediates for glycolysis?

A

fructose-1,6-biphosphate and 2x triode phosphate

95
Q

What are the three stages of glycolysis?

A
  • glucose trapped and destabilised
  • 2x 3C molecules are formed
  • ATP is generated
96
Q

How many ATP are made in glycolysis?

A

2 ATP

97
Q

What are the three enzymes in glycolysis and what are their roles?

A
  • hexokinase (substrate entry)
  • phosphofructokinase (rate of flow)
  • pyruvate kinase (product exit)
98
Q

What are the factors that affect glycolysis?

A

+ AMP

  • ATP
  • citrate
  • H+
99
Q

What is the ATP/AMP ratio?

A

the energy charge
if it is all ATP then it is charged
if it is all AMP and Pi then it is discharged

100
Q

What happens if there is no oxygen for respiration?

A

NADH converts pyruvate to lactate
NADH is then regenerated in the ETC
this can then be used in glycolysis

101
Q

How does pyruvate get into the mitochondrial matrix?

A

H+ gradient
H+/pyruvate symport
facilitated diffusion

102
Q

How is pyruvate then changed?

A

pyruvate —pyruvate dehydrogenase complex—> acetyl-CoA + NADH + H+ + CO2

103
Q

What is the enzyme of the TCA cycle that in the membrane?

A

succinate dehydrogenase is in the membrane and makes FADH2

104
Q

What does one molecule of glucose make up until the TCA cycle?

A 
4ATP
10NADH
10H+
2FADH2
6CO2
105
Q

What comes out of one turn of the TCA cycle?

A

3NADH
2CO2
1FADH2
1GTP

106
Q

What do electrons from NADH and FADH2 do?

A

convert O2 to H2O and H+ is moved across the membrane

these then flow back to make ATP

107
Q

What is the malate-aspartate shuttle for?

A

moves NADH from cytoplasm to matrix

108
Q

What happens in the malate-aspartate shuttle?

A
  • aspartate –> oxaloacetate -(NADH to NAD)-> malate
  • malate transferred to matrix
  • malate -(NAD to NADH)-> oxaloacetate –> aspartate
    (malate from TCA cycle also used)
109
Q

What is the phosphoryl transfer potential?

A

deltaG for the hydrolysis of ATP

110
Q

What is the electron transfer potential?

A

the redox potential of a compound so how readily it donates an electron

111
Q

What does a negative or a positive electron transfer potential mean?

A

-ve means it will donate electrons

+ve means it will accept electrons

112
Q

What are the two steps of ETC?

A

electron transport

ATP synthesis

113
Q

How are electrons transported in the ETC?

A

e- from NADH and FADH2 to O2]energy pumps H+ out

114
Q

How is ATP synthesised in the ETC?

A

H+ gradient

H+ comes through ATP synthase

115
Q

How to electrons move across membrane?

A

complexes eg cytochromes with haem group

3 of 4 pump H+

116
Q

What is the electrochemical gradient?

A

+ve inside membrane
-ve in matrix
so electrons move inside the membrane

117
Q

How is the ETC inhibited?

A

cyanide, azide, CO = stops electron transfer
no H+ gradient
no ATP made

118
Q

How many ATP does one glucose make?

A

30-32 ATP

119
Q

What is the P/O ratio?

A

a measurement of coupling of ATP synthesis to electron transport
eg P/O of NADH is 2.5

120
Q

What does ATP yield depend on?

A

P/O values

and on which shuttle is used to move NADH into matrix

121
Q

What is the FiFoATPase?

A

a proton pore that uses energy from the return of protons along their electrochemical gradient in a condensation reaction with ADP and Pi to make ATP

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