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Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

define van der waals

A

interaction of electrons of non-polar substances

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2
Q

define electronegativity

A

ability to gain electrons- attraction of the nucleus

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3
Q

define catabolism

A

break down of molecules

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4
Q

define anabolism

A

synthesis of molecules

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5
Q

define exergonic

A

release of energy

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6
Q

define endogonic

A

requires energy

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7
Q

first law of thermodynamics

A

conservation of energy

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8
Q

second law of thermodynamics

A

energy transferral is not 100% efficient

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9
Q

reactions involve change in three things

A
  1. enthalpy
  2. entropy
  3. free energy
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10
Q

define exergonic reactions

A

products have less energy than reactants. energy change is negative. these reactions can be spontaneous.

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11
Q

define endogenic reactions

A

products have more energy than reactants. free energy change is positive. an input of energy is needed

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12
Q

amount of energy at the completion of equilibrium

A

more energy

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13
Q

hydrophilic electrostatic attractions

A
  1. ion-dipole interactions

2. dipole-dipole interactions

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14
Q

describe the primary structure of a protein

A

sequence of amino acid residues

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15
Q

describe the secondary structure of a protein

A

formation of a polypeptide backbone

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16
Q

describe the tertiary structure of a protein

A

3D structure

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17
Q

quaternary structure

A

spatial arrangement of polypeptide chains

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18
Q

where can polypeptides rotate

A
  1. alpha-carbon and amino group

2. alpha-carbon and carboxyl group

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19
Q

three types of secondary structures can be made

A
  1. alpha-helix: hydrogen bonds formed between -N-H and -C-O
  2. beta-sheets: anti-parallel strands, zig-zag structure
  3. triple helix: three helices with the same axises.
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20
Q

characteristics of fibrous proteins

A

long fibres, strong, insoluble e.g. keratin and collagen

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21
Q

characteristics of globular proteins

A

spherical shape, soluble,

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22
Q

forces that stabilise the tertiary structure

A
  • electrostatic attractions
  • hydrophobic interactions
  • H-bonds
  • disulphide bonds
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23
Q

define chaperones

A

proteins that aid folding of other proteins

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24
Q

factors that cause denaturation

A
  • heat
  • pH
  • detergents
  • thiol agents
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25
Q

examples of purines

A

A and G

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26
Q

examples of pyrimidines

A

U, C and T

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27
Q

which carbon does the OH group join to?

A

3’ carbon

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28
Q

which carbon does the phosphate group join to?

A

5’ carbon

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29
Q

which carbon is free to allow synthesis?

A

3’ carbon

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30
Q

name of DNA replication

A

semi-conservative

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31
Q

features to ensure DNA replication finishes quickly

A
  1. bidirectional
  2. free 3’ on the leading strand
  3. use of lagging strands and Okazaki fragments
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32
Q

define DNA ligase

A

enzyme that forms a phosphodiester bond

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33
Q

three classes of RNA

A
  • rRNA
  • tRNA
  • mRNA
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34
Q

structure of tRNA

A

contains an anticodon, specific amino acid attaches to the 3’ end, cloverleaf shape.

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35
Q

five steps of transcription

A
  1. RNA polymerase binding
  2. DNA chain separation
  3. initiation
  4. elongation
  5. termination
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36
Q

describe the structure of promotor regions

A

contain a TATA box. the TATA box binding protein induces a kink in DNA which determines the start and direction.

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37
Q

which enzyme unwinds DNA?

A

DNA helicases

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38
Q

what does initiation require?

A

transcription factors

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39
Q

describe the process of elongation in transcription

A

DNA is unwound by RNA polymerase. It is synthesises in the 5’-to-3’ direction. Complementary to the template strand.

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40
Q

describe the process of termination in transcription

A

stem-loop structure is made followed by a line of U’s so a specific enzyme cleaves the RNA. Polymerase dissociates.

41
Q

two functional domains of transcription factors are

A
  • DNA binding domain

- transcriptional activation domain

42
Q

define splicing

A

removal of introns

43
Q

the end of the mRNA is processed by

A
  • addition of poly(A) tail
  • addition of a 5’ cap
    these stabilise the mRNA
44
Q

name the enzyme that binds amino acids to their corresponding tRNA molecules

A

aminoacyl-tRNA synthetases

45
Q

three binding sites on ribosomes

A
  1. E (exit)
  2. P (peptidyl)
  3. A (aminoacyl)
46
Q

stages of translation

A
  1. initiation
  2. elongation
  3. termination
47
Q

describe initiation in translation

A

small subunit of the ribosome binds to the 5’ end of the mRNA and the large subunit joins once the tRNA is located in the P site

48
Q

describe the process of elongation in translation

A

elongation factor brings the next aminoacyl-tRNA to the A site. GTP hydrolysis allows the EF to be released.

49
Q

describe the process of the peptide bond formation

A
  1. peptidyl transferase catalyses the peptide bond formation between P and A.
  2. EF moves ribosome along mRNA
  3. empty tRNA moves to E site and is removed
50
Q

describe the process of termination in translation

A

occurs when the A site encounters a stop codon

51
Q

describe the types of base mutations

A
  1. point: change in a single base
  2. missense: change in amino acid sequence
  3. nonsense: creates a termination code
  4. silent: no change (degenerate)
  5. frameshift: changes reading frame
52
Q

types of chromosomal mutations

A
  • deletions
  • duplication
  • inversions
  • translocations
53
Q

three things that can happen to the finished protein

A
  1. targeted (moved to final destination)
  2. modification
  3. degradation
54
Q

free ribosomes made proteins destined for?

A
  • cytosol
  • nucleus
  • mitochondria
55
Q

bound ribosomes make proteins destined for?

A
  • membrane
  • ER
  • Golgi
56
Q

function of an enzymes

A

speeds up the rate at which a reaction reaches equilibrium without being used up or affecting the position of equilibrium.

57
Q

characteristics of enzymes

A
  • protein
  • catalysts
  • efficient
  • specific
  • potent
58
Q

define a coenzyme

A

organic molecules that only associate with enzymes transiently

59
Q

define a cofactor

A

enzyme that has a metal coordination (metalloprotein)

60
Q

an enzyme without a cofactor is called?

A

apoenzyme

61
Q

apoenzyme + cofactor

A

holoenzyme

62
Q

ways an enzyme can be regulated

A
  1. phosphorylation- active or inactive form carried out by kinases and phophatases
63
Q

define a zymosen

A

inactive precursors of an enzyme

64
Q

define Km

A

concentration in moles of the substrate when at 1/2 Vmax.

65
Q

define Vmax

A

maximum velocity of a reaction

66
Q

two types of reversible enzyme inhibition

A
  1. competitive (orthosteric site)

2. non-competitive (allosteric site)

67
Q

irreversible enzyme inhibition

A

non-competitive causes bond breakage

68
Q

effect on Vmax and Km during competitive inhibition

A

Vmax does not change, Km varies

69
Q

effect on Vmax and Km during non-competitive inhibition

A

Vmax varies and Km does not change

70
Q

define feedback inhibition

A

inhibition of rate limiting enzymes (mechanism of allosteric control

71
Q

four pathways glucose can be used in

A
  1. aerobic glycolysis
  2. anaerobic glycolysis
  3. pentose phosphate pathway
  4. storage
72
Q

how is glucose transported into the cell?

A

co-transport using Na+/glucose symporters (GLUT-1)

73
Q

describe the three stages of glycolysis

A
  1. glucose is trapped and destabilised by the addition of phosphates
  2. two 3-carbon molecules are formed
  3. generation of ATP
74
Q

products of glycolysis are?

A
  1. 2 pyruvate
  2. 2 net ATP
  3. 2NADH + 2H+
75
Q

enzymes involved in glycolysis

A
  1. hexokinase (glucose to glucose 6-phosphate)
  2. phosphofructokinase controls rate of flow
  3. pyruvate kinase (pyruvate formed)
76
Q

inhibitors of phosphofructokinase (PFK)

A

ATP
citrate
H+

77
Q

define energy charge

A

ATP/ AMP

78
Q

define the Warburg effect

A

regulation of anaerobic glycolysis in cancer cells. produces high rate of glucose to lactate.

79
Q

for glycolysis to continue what must happen to the product NADH

A

it must be deoxidised to NAD+

80
Q

location of the TCA cycle

A

mitochondria

81
Q

location of glycolysis

A

cytoplasm

82
Q

how does pyruvate enter the mitochondrial matrix

A

H+ gradient from cytosol to matrix using pyruvate transporters (symporters)

83
Q

which enzyme catalysed the decarboxylation of pyruvate

A

pyruvate dehydrogenase complex

84
Q

products of the link reaction

A
  1. NADH + H+

2. acetylCoA

85
Q

characteristics of the TCA cycle

A
  • 8 reactions
  • 1 GTP formed
  • 3 NADH
  • 1 FADH2
  • 2 CO2
  • the cycle turns twice for each mole of glucose
86
Q

what is the 6-carbon molecule in the TCA cycle called

A

citric acid

87
Q

what is the 4-carbon molecule in the TCA cycle called

A

oxaloacetic acid

88
Q

what does one mole of glucose produce in the TCA cycle? (only electron transporters)

A

10NADH
10H+
2FADH2

89
Q

final destination of electrons

A

reduces O2 to H2O

90
Q

describe how NADH moves from the cytosol to the mitochondrial matrix

A
  • NADH is used to generate malate from oxaloacetate
  • malate transporters transfer malate to the matrix
  • malate is converted back to oxaloacetate generating NADH
91
Q

define phosphoryl transfer potential

A

free energy after the hydrolysis of ATP

92
Q

define electron transfer potential

A

how readily a substance donates an electron

93
Q

two stages of the chemiosmotic theory

A
  1. electron transport

2. ATP synthesis

94
Q

characteristics of the electron transport respiratory chain

A
  • four multisubunit complexes on the inner mitochondrial membrane
  • electrons from NADH enter at complex 1
  • electrons from FADH2 enter at complex 2 (TCA cycle)
  • electrons are transferred to O2 to form H2O
95
Q

subunits names

A

Q and cytochrome C

96
Q

define cytochromes

A

proteins that contain a haem group. the Fe2+ can take up and release electrons

97
Q

describe the H+ gradient

A

more protons in the inter membrane space so they flow back to the matrix via ATP synthase channels

98
Q

structure of ATP synthase

A
  • F1 protrudes into the matrix
  • F0 is in the inner membrane (proton channel)
  • stator
  • rotor (turns during proton flow)
99
Q

inhibitors of oxidative phosphorylation

A
  • cyanide
  • azide
  • CO

Principles (11 decks)

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