Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

My Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What are the four most common biochemical reactions?

A

phosphorylation
acylation
carboxylation
esterification

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the most electronegative species?

A

oxygen so it is the terminal electron acceptor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the main functions of biomolecules?

A 
information storage
structure
energy generation
energy storage
recognition/ communication/ specificity
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the major classes of biomolecules?

A

peptides/protreins
lipids
nucleic acids
carbohydrates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the first law of thermodynamics?

A

energy is neither created nor destroyed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the second law of thermodynamics?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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])
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Why is ATP unstable?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is catabolism?

A

breaking down larger molecules into smaller ones releasing energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is anabolism?

A

making large molecules from small ones using energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What type of reaction is used as a control point?

A

large dGs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the direction of a peptide?

A

N –> C bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

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

A

20 L amino acids with an alpha carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Why are peptide bonds partially double?

A

the lone pair on N can become a C=N

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the Henderson-Hasselbalch equation?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What does pH equal in a buffer solution?

A

pKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is the isoelectric point?

A

the pH where a molecule has no net charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are the extra bonds in an alpha helix?

A

every 4th makes a hydrogen bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What breaks alpha helices?

A

proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is a nucleoside?

A

base and sugar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is a nucleotide?

A

nucleoside and one or more phosphate groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What are the purines?

A

Adenine and Guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are the pyrimidines?

A

Uracil, Thymine and Cytosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What makes up a phosphodiester bond?

A

between 3’ OH group and 5’ triphosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What end are nucleotides added at?

A

3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

How many hydrogen bonds between the bases?

A

A two bonds to T

C three bonds to G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is needed to start DNA replication?

A

RNA primer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What makes the RNA primers that are needed for replication?

A

primase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What is exonuclease activity?

A

removal of the incorrect nucleotides if an error is made

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

How many types of RNA polymerase does a cell have?

A

Eukaryotic have three

Prokaryotic have one

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are telomeres?

A

repeat sequences of DNA that protect the chromosome ends

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What does telomerase do?

A

extends telomeres (cancer cells reactivate this)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

What does newly-formed RNA look like?

A

stem-loop structure and a stretch of Us when released

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What do enhancers do?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What is capping?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What are the three binding sites of a ribosome?

A

Exit
Peptidyl
Aminoacyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What happens in initiation of translation?

A
  • GTP hydrolysed for energy

- initiator tRNA is in P site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

My Principles (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions