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Biochemistry > M1: Proteins > Flashcards

M1: Proteins Flashcards

1
Q

What can we learn from a progress curve of an enzyme catalyst reaction?

A

It measures the appearance of product with time at steady rate.

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2
Q

What is the relationship between V vs [S] on a V vs [S] curve for an enzyme catalysed reaction at low substrate concentration?

A

increases in a linear way at first but as all the enzyme active sites become occupied, the rate of the reaction stops increasing.

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3
Q

When there is an excess of substrate, reaction velocity is ___ to enzyme concentration.

A

proportional

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4
Q

What 2 kinetic parameters can be identified on a V vs [S] curve?

A
  1. Vmax = maximum velocity possible, when [S] = infinity

2. Km= the substrate concentration at which Vobs = Vmax/2

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5
Q

Why does an enzyme catalysed reaction reach maximum velocity when there is excess substrate but a fixed concentration of enzyme?

A

It is more likely to successfully bump into and combine to the substrate if there is a higher concentration

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6
Q

What equation can be used to describe a V vs [S] curve for monomeric enzymes?

A

Michaelis-Menten equation

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7
Q

What assumption can be made to simplify a Michaelis-Menten model reaction?

A

Haldane’s steady state assumption: the rate of ES formation equals the rate of its breakdown.

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8
Q

What are allosteric enzymes?

A

Enzymes respond to effectors binding away from the active site. This binding accompanies a change of shape, which in turn changes enzymatic activity. They often have multiple subunits and display cooperative behaviour.

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9
Q

Do allosteric enzymes follow the Michaelis-Menten model? Why/Why not?

A

no - it plots a sigmoidal curve as it responds more steeply to intermediate changes in [S]. The evolve at regulatory points in metabolic pathways.

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10
Q

What are some examples of allosteric enzymes and what type of pathways are they important in?

A

Phosphorfructokinase controls glycolysis `

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11
Q

What are zymogen and why are they important?

A

They are secreted from the pancreas in inactive form. Cleavage by proteases in the gut produces active enzymes. Temporal and spatial control.

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12
Q

what is plotted on a Lineweaver-Burk plot?

A

[S] vs Vmax

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13
Q

What does the y-intercept represent on a Lineweaver-Burk plot?

A

1/Vmax

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14
Q

What does the x-intercept represent on a Lineweaver-Burk plot?

A

-1/Km

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15
Q

What is the significance of Km?

A

Is the substrate concentration needed to reach half Vmax

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16
Q

What does a high Km for an enzyme-substrate pair indicate?

A

low affinity

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17
Q

If an enzyme has multiple substrates, how can we use Km to determine substrate preference?

A

Finding the Km value for hexokinase in ATP and glucose and glucokinase in glucose

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18
Q

What does Kcat for an enzyme catalysed reaction represent?

A

Number of substrate molecules converted to product, per enzyme, per unit of time, when E is saturated. Therefore, helps to define the activity of one enzyme molecule (catalytic activity)

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19
Q

How do we define catalytic efficiency?

A

Kcat/Km
most efficient will have…
> High Kcat ( turnover a lot of substrate into product)
> Low Km (low substarte conc required to achieve near Vmax; high affinity)

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20
Q

For what purpose are transition state analogues designed?

A

makes tight binding inhibitors

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21
Q

What are the 2 main classes of inhibitors and how do they differ in their binding to an enzyme?

A

Irreverable:
> permanently binds to enzyme through covalent bond and inactivates it permanently
Reversible:
> Binds to enzyme through a non-covalent bond but can subsequently be released, leaving the enzyme in its original condition

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22
Q

Competitive vs Pure non-competitive inhibition.

A

Michaelis-Menten Plot:
> inhibited will rise quickly
> Competitive will be in the middle
> Non-competitive will be smaller and less
Lineweaver-Burk Plot
> Competitive and uninhibited with have the same intersection
> non-competitive will be above

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23
Q

What is a receptor protein?

A

A cellular protein that controls chemical signalling between and within cells

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24
Q

How do receptors differ from enzymes?

A

> Enzymes generally have 1 active site where receptors have several
Enzymes bind substrates where receptors bind ligands
Enzymes change substrate into product where receptors release ligands unchanged

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25
Q

What are the 3 receptor classes?

A
  1. Ligand-gated ion channel
  2. G protein-coupled receptor (GPCR)
  3. Receptor tyrosine kinase
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26
Q

What is a ligand?

A

Chemical substance that specifically binds to a receptor

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27
Q

What is the difference between endogenous ligands and exogenous ligands?

A

Endogenous ligands are produced int he body whereas exogenous ligands are drugs and toxins

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28
Q

Activation and inhibition will only occur when…

A

the pairing is correct

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29
Q

What is an agonist?

A

Chemical substance (ligand) that binds to a receptor and activates it

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30
Q

What is signal transduction?

A

Active receptor starts a chain of events where messages are passed on through the cell

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31
Q

What is an antagonist?

A

Chemical substance (ligand) that binds to a receptor and prevents activation by an agonist

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32
Q

What are the common principles behind activation or inhibition of proteins?

A
  1. Chemical Substance
  2. Binds ot protein
  3. Causes inhibition or activation
  4. Changes cellular response
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33
Q

Most receptors are found on the inside/outside of the cell where they act as sensors of the intracellular/extracellular envrionment.

A

Outside & extracellular

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34
Q

What is the advantage of the receptor being located where it is?

A

act as sensors

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35
Q

Are ligand-receptor interactions specific or non-specific?

A

specific

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36
Q

Are endogenous ligands more likely to be agonist r antagonists?

A

agonist

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37
Q

What is a second messenger?

A

multi-step pathways that provide opportunities for coordination and regulation of cellular responses. They can be proteins or chemical signals

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38
Q

Do different receptor types use the same signal transduction processes?/

A

yes -
GAs = stimulates (increase)
GAi = inhibits (decrease)

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39
Q

How is phosphorylation and dephosphorylation important in signal transduction pathways?

A

Phosphorylation uses protein kinases to transfer phosphates from ATP to protein. Dephosrylation rapidly removes the phosphates from proteins to carefully control signal transduction

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40
Q

Give a reason why ligand-gated ion channels provide faster signalling than GPCRs ad RTKs?

A

ions directly flow through the channel into the cell to produce effects

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41
Q

Explain how the same receptors on different cell types mediate different responses

A

Different cells have different collections of receptors and relay molecules, allowing cells to detect and respond differently to different ligands. The sam ligand/receptor pairing can have different effects in different cells because they use different combinations of relay molecules for signal transduction

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42
Q

Outline the signal transduction mechanism for the insulin receptor in muscle/adipose tissue compared to liver cells

A

In muscle and adipose cells - the receptor activation causes phosphorylation of “adaptor” protein a further signal transduction evets, leading to GLUT-4 translocation.
In liver cells - the receptor activation causes phosphorylation of an “adaptor” protein, and further signal transduction events, this time leading to glycogen synthesis.

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43
Q

Outline the signal transduction for the glucagon receptor on liver cells

A

Receptor activation causes G protein activation and further signal transduction events, leading t glycogen breakdown

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44
Q

What is the role of GLP-1?

A

Receptor activation causes G protein activation and further signal transduction events, lading to insulin secretion.

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45
Q

What are proteins polymers of?

A

non-brnaching polymers made up of a specific sequence of amino acids in varying lengths.

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46
Q

How many standard amino acids are there?

A

20

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47
Q

What is the name of the bond that links amino acids in the polypeptide chain?

A

peptide bond

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48
Q

Does each protein have an unique sequence of amino acids? Explain

A

yes - to carry out different functions (?)

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49
Q

Why is it important to know and understand protein structure?

A

It is key to understanding the biochemistry of life.

50
Q

What are the main techniques used to determine protein structure?

A

> Protein crystallography
Electron cyro-microscopy
NMR spectroscopy

51
Q 
Name a protein that is involved in:
DNA replication 
RNA replication 
Oxygen transport 
Immune protection 
Digestion 
Metabolism
A 
> DNA polymerase 
> RNA polymerase 
> Hemoglobin 
> Antibodies 
> Trypsin, amylase 
> Alcohol dehydrogenase, Hexokinase
52
Q

The names of the amino acids can be abbreviated in both _ letter and _ letter codes.

A

3, 1

53
Q

What does “amino acids are chiral” mean?

A

they are non-superimposable mirror images of each other

54
Q

What are the 4 main groups of amino acids, as discussed?

A

> non-polar amino acids
-vely charged (acidic) polar amino acids
+vely charged (basic) polar amino acids
Uncharged polar amino acids

55
Q

What are the properties of non-polar amino acids?

A

> Amino group
Acidic group
Attached to a carbon
Side chain

56
Q

Where in a protein would you expect to find non-polar amino residues?

A

?

57
Q

What chemical groups would we expect to find in the R-group of an ionisable amino acid?

A

?

58
Q

Where in a protein would we often find ionisable amino residues?

A

amino and carboxyl ends of amino acids

59
Q

What is the name of the bond that links amino acids in the polypeptide chain?

A

peptide bond

60
Q

What are the key properties of the peptide bond?

A

> 40% double bond charcter, leads to planarity
rotational barrier
dipole
predominantly trans

61
Q

Define pKa and pI, what can these values tell us about an amino acid side chain?

A

pKa value for an ionsible group on an amino acid or protein is the pH at which the group is 50% ionised.
pI or isoelectric point is the pH at which the net charge on an amino acid is zero

62
Q

List some common examples of post-transitional modifications.

A 
> Phosphorylation 
> Hydroxylation 
> Carboxylation 
> Metal Bonding
> Iodination 
> Glycosylation
63
Q

What are some important functions of post-transitional modifications?

A

Phosphorylation: often used to control enzyme activity like a chemical ON/OFF switch
Hydroxylation: needed to prevent connective tissues diseases and scurvy, often proline and lysine involved
Carboxylation: needed for blood clotting, often glutamate involved.

64
Q

List the levels of protein structure and define what each one means

A

Primary - amino acid sequence of a protein
Secondary - local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues
Tertiary - 3D structure of a complete protein chain
Quaternary - interchain packing and structure for a protein that contains multiple protein chains.

65
Q

In what context would we encounter the terms phi and psi?

A

phi - rotation angle around N-C bond. Can lead to O-O collision.
psi - rotation angle around C-C bond. Can lead to NH-NH collisions

66
Q

What are the key properties of an a-helix?

A 
> 3.6 residues/turn, 5.4 rise/turn, 1.5 residue
> spiral is "right handed"
> side chains point out from the helix 
> stabilising hydrogen bonds
> "helix breakers" 
> helix dipole exists
67
Q

What are the key properties of b-helix?

A

> peptide chains with a more extended structure than the a-helix
H-bonding occurs between adjacent chains
Typically 2-10 strands per sheet
Average strand length contains 6 amino acid residues.
may have up to 15 residues
2 types of H-bonding interaction in a B-sheet.

68
Q

What is a beta turn and what are the key features?

A

> needed to form globules
often short, hairpin like, involve usually 3 or 4 residues
High Gly, Pro content
Almost 30% residues involved in turns
H-bond, across the turn is common
more than 16 types, given Roman numeral names
Type I, Type II are very common types

69
Q

Define supersecondarry structure and list some examples of common supersecondary structure motifs.

A 
elements of secondary structure are connected by turns or by regions of less ordered structure called loops or coils. 
>Helix - turn - helix 
> B hairpin
> Greek key 
> Strand-helix-strand
70
Q

What is a protein domain motif?

A

Hydrophobic core and the hydrophilic parts of the protein are arranged on the surface in contact or near solvent.

71
Q

What is a protein family, and what are some common examples of such families?

A

alpha: mostly helical, globin fold
alpha/beta: mix of a and b structure. Horseshoe
Anti-parallel b family: Most antiparallel B structure

72
Q

Describe Anfinsen’s experiment

A

Exposed the native enzyme to excess beta mercaptoethanol

73
Q

What conclusions can be made from Anfinsen’s experiment regarding protein folding?

A

They unfold and refold even when it was folded the wrong way, it would fix itself.

74
Q

Protein folding is a random process - True/False?

A

True

75
Q

What are the key steps involved in the folding of a protein?

A
  1. Formation of short secondary structure segments
  2. Nuceli or subdomains
  3. Subdomains come together to form a partly folded domain; a “molten globule” that can rearrange
  4. Final domain structure emerges, small conformational adjustments to give final compact native structure
76
Q

How is protein fold stabilised?

A

Non-covalent interaction, additional covalent bonds, hydrophobic core.

77
Q

What is a chaperone and what role do they play?

A

proteins that assist i folding/ unfoldong and the assembly/disassembly

78
Q

What factors can lead to protein unfolding?̄̉

A

weakening of non-covalent interactions

79
Q

Give examples of diseases associated with protein unfolding

A 
BSE
CJD
Kuru 
Alzeimers disease 
Type 2 diabetes
80
Q

What is the main role of myoglobin?

A

facilitates release of oxygen to the muscle

81
Q

What is the main role of haemoglobin?

A

Transferring oxygen from lungs to tissues through the blood

82
Q

What are the major components of myoglobin or haemoglobin molecule?

A

> oxygen binds to iron of haem
Shift from dull to bright red allowing monitoring O2 binding
Affinity for oxygen is altered by molecules binding elsewhere

83
Q

What is a haem group and what are its properties?

A

Binding of oxygen to the Fe2+

84
Q

How many subunits make up myoglobin vs haemoglobin?

A

Myoglobin:
> Monomer
Haemoglobin:
> tetramer

85
Q

What secondary structure dominates the globin protein?

A

8 a-helices A-H and connecting loops

86
Q

Fe2+ has 6 coordination bind sites, what binds to each of these sites?

A

4 to nitrogen of haem
1 to nitrogen of histidine F8 of the globin
1 to the 02

87
Q

What is the role of His E7 myoglobin?

A

Distorts binding of gas molecules to 6th coordination position on haem Fe2+

88
Q

Myoglobin is O2 saturated at low/high pO2 and realeases O2 at low/high pO2

A

low

low

89
Q

Describe the alternate side-chain packing in R- and T-state haemoglobin

A

T-State: deoxyhaemoglobin

R-state: oxyhaemoglobin

90
Q

What is an allosteric regulator?

A

modulating the activity of a protein by the binding of a ligand, called an effector, to an active site

91
Q

Haemoglobin is under allosteric control by which molecule?

A

BPG

92
Q

How does the compound BPG modify the O2 binding characteristics of haemoglobin?

A

Binds to deoxy-Hb by electrostatic interaction. It then stabilises Hb in the deoxy T-state, reducing oxygen affinity. It is produces during respiration in peripheral tissues, so promotes oxygen release where needed.

93
Q

Whys is the O2 saturation curve for haemoglobin sigmoidal?

A

The binding of the 1st O is harder than the rest

94
Q

Why does the conformation of haemoglobin change on O2 binding?

A

Brought closer

95
Q

How does shifting from the R-state to the T-state affect how globin interacts with the haem molecule?

A

increases coopertivity

96
Q

Name 2 factors, other than the allosteric regulator, that facilitate the release of O2

A

CO2 and H+

97
Q

What is the Bohr effect?

A

hemoglobin’s lower affinity for oxygen secondary to increases in the partial pressure of carbon dioxide and/or decreased blood pH

98
Q

How are the oxygen binding properties of foetal haemoglobin different to that in adult haemoglobin?

A

Foetal haemoglobin includes alternate isoforms with higher affinities for O2. This allows for the foetus to capture oxygen in the placenta. Foetal lack an amino acid in the BPG binding site, so bind BPG less well.

99
Q

In what state is the Fe atom in methemoglobin? Does this lead to any effect in regards to haemoglobin’s ability to bind oxygen?

A

Fe3+

100
Q

Will a biological process occur spontaneously if △G>0? Why/why not?

A

no - requires energy and the substrates dominate.

101
Q

Do enzymes alter the eqbm of a reaction?

A

Yes

102
Q

What is a transition state in relation to an enzyme catalysed reaction?

A

Highest energy along the reaction coordinate

103
Q

Does an enzyme bind the substrate to the transition state more tightly?

A

yes

104
Q

How is the progression of a reaction through the transition state affected by the presence of an enzyme?

A

The transitions state will have decreased as the activation energy has decreased

105
Q

What are the 2 models used to describe enzyme-substrate binding?

A

Lock and Key
and
Induced-fit model

106
Q

How are these 2 models different/similar to each other

A

Lock and key has the active site and the substrate with the same same whereas the induced-fit model change their shape when the substrate binds and the active site becomes complementary to the shape of the substrate.

107
Q

Why do we need a formal classification system for enzymes?

A

be able to show the properties of the substrates

108
Q

What types of bonds might we find between an enzyme and substrate?

A

> Ionic bonds
Hydrogen bonds
Van der Waals Interactions
Covalent bonds

109
Q

How is △Gº⇞ lowered?

A
  1. Ground state destabilisation
  2. Transition state stabilisation
  3. Alternate reaction pathway with a different transition state
110
Q

What is a cofactor, and what purpose do they serve?

A

confer specific abilities

111
Q

What is a coenzyme and how it derived?

A

Small organic molecules, co-substrates, carriers and often derived form vitamins

112
Q

How do coenzymes aid in enzymatic reactions?

A

Turning substrates into products

113
Q

Why are proximity and orientation effect so vital in enzymatic catalysis?

A

they have to be close together and in the right orientation or the reaction will not occur.

114
Q

What is covalent catalysis?

A

Formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme

115
Q

What are electrophiles and nucleophiles and what form of catalysis are they involved in?

A

nucleophiles donate an electron pair whereas electrophiles accept electron pairs. They drive covalent catalysis.

116
Q

What type of amino acids are likely to be involved in acid-base catalysis?

A

Glu, Asp

Lys, Arg

117
Q

Covalent catalysis involves the formation of what kind of intermediate interaction with the enzyme?

A

tetrahedral

118
Q

What is a protease, and what is the difference between a serine protease and an aspartate protease?

A

proteases break the peptide binds of proteins.

119
Q

What are the important amino acid residues in the active site of chymotrypsin?

A

Serine superimposes backbone whereas chymotrypsin does not

120
Q

The active site of chymotrypsin contains an oxyanion hole and a specifity pocket. what are these and why are they important?

A

Oxyanion hole stabilises tetrahedral intermediate which lowers the activation energy.
Specify pocket is a binding pocket which which determines the specificity of the protease.

121
Q

Briefly outline the catalytic mechanism of chrymotrypsin

A

> nucleophilic attack and covalent catalysis

> Stabilised transition state at the end of the 1st half reaction

Biochemistry (3 decks)

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