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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
What are the 3 receptor classes?
1. Ligand-gated ion channel 2. G protein-coupled receptor (GPCR) 3. Receptor tyrosine kinase
26
What is a ligand?
Chemical substance that specifically binds to a receptor
27
What is the difference between endogenous ligands and exogenous ligands?
Endogenous ligands are produced int he body whereas exogenous ligands are drugs and toxins
28
Activation and inhibition will only occur when...
the pairing is correct
29
What is an agonist?
Chemical substance (ligand) that binds to a receptor and activates it
30
What is signal transduction?
Active receptor starts a chain of events where messages are passed on through the cell
31
What is an antagonist?
Chemical substance (ligand) that binds to a receptor and prevents activation by an agonist
32
What are the common principles behind activation or inhibition of proteins?
1. Chemical Substance 2. Binds ot protein 3. Causes inhibition or activation 4. Changes cellular response
33
Most receptors are found on the inside/outside of the cell where they act as sensors of the intracellular/extracellular envrionment.
Outside & extracellular
34
What is the advantage of the receptor being located where it is?
act as sensors
35
Are ligand-receptor interactions specific or non-specific?
specific
36
Are endogenous ligands more likely to be agonist r antagonists?
agonist
37
What is a second messenger?
multi-step pathways that provide opportunities for coordination and regulation of cellular responses. They can be proteins or chemical signals
38
Do different receptor types use the same signal transduction processes?/
yes - GAs = stimulates (increase) GAi = inhibits (decrease)
39
How is phosphorylation and dephosphorylation important in signal transduction pathways?
Phosphorylation uses protein kinases to transfer phosphates from ATP to protein. Dephosrylation rapidly removes the phosphates from proteins to carefully control signal transduction
40
Give a reason why ligand-gated ion channels provide faster signalling than GPCRs ad RTKs?
ions directly flow through the channel into the cell to produce effects
41
Explain how the same receptors on different cell types mediate different responses
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
42
Outline the signal transduction mechanism for the insulin receptor in muscle/adipose tissue compared to liver cells
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.
43
Outline the signal transduction for the glucagon receptor on liver cells
Receptor activation causes G protein activation and further signal transduction events, leading t glycogen breakdown
44
What is the role of GLP-1?
Receptor activation causes G protein activation and further signal transduction events, lading to insulin secretion.
45
What are proteins polymers of?
non-brnaching polymers made up of a specific sequence of amino acids in varying lengths.
46
How many standard amino acids are there?
20
47
What is the name of the bond that links amino acids in the polypeptide chain?
peptide bond
48
Does each protein have an unique sequence of amino acids? Explain
yes - to carry out different functions (?)
49
Why is it important to know and understand protein structure?
It is key to understanding the biochemistry of life.
50
What are the main techniques used to determine protein structure?
> Protein crystallography > Electron cyro-microscopy > NMR spectroscopy
51
``` Name a protein that is involved in: DNA replication RNA replication Oxygen transport Immune protection Digestion Metabolism ```
``` > DNA polymerase > RNA polymerase > Hemoglobin > Antibodies > Trypsin, amylase > Alcohol dehydrogenase, Hexokinase ```
52
The names of the amino acids can be abbreviated in both _ letter and _ letter codes.
3, 1
53
What does "amino acids are chiral" mean?
they are non-superimposable mirror images of each other
54
What are the 4 main groups of amino acids, as discussed?
> non-polar amino acids > -vely charged (acidic) polar amino acids > +vely charged (basic) polar amino acids > Uncharged polar amino acids
55
What are the properties of non-polar amino acids?
> Amino group > Acidic group > Attached to a carbon > Side chain
56
Where in a protein would you expect to find non-polar amino residues?
?
57
What chemical groups would we expect to find in the R-group of an ionisable amino acid?
?
58
Where in a protein would we often find ionisable amino residues?
amino and carboxyl ends of amino acids
59
What is the name of the bond that links amino acids in the polypeptide chain?
peptide bond
60
What are the key properties of the peptide bond?
> 40% double bond charcter, leads to planarity > rotational barrier > dipole > predominantly trans
61
Define pKa and pI, what can these values tell us about an amino acid side chain?
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
List some common examples of post-transitional modifications.
``` > Phosphorylation > Hydroxylation > Carboxylation > Metal Bonding > Iodination > Glycosylation ```
63
What are some important functions of post-transitional modifications?
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
List the levels of protein structure and define what each one means
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
In what context would we encounter the terms phi and psi?
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
What are the key properties of an a-helix?
``` > 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
What are the key properties of b-helix?
> 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
What is a beta turn and what are the key features?
> 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
Define supersecondarry structure and list some examples of common supersecondary structure motifs.
``` 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
What is a protein domain motif?
Hydrophobic core and the hydrophilic parts of the protein are arranged on the surface in contact or near solvent.
71
What is a protein family, and what are some common examples of such families?
alpha: mostly helical, globin fold alpha/beta: mix of a and b structure. Horseshoe Anti-parallel b family: Most antiparallel B structure
72
Describe Anfinsen's experiment
Exposed the native enzyme to excess beta mercaptoethanol
73
What conclusions can be made from Anfinsen's experiment regarding protein folding?
They unfold and refold even when it was folded the wrong way, it would fix itself.
74
Protein folding is a random process - True/False?
True
75
What are the key steps involved in the folding of a protein?
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
How is protein fold stabilised?
Non-covalent interaction, additional covalent bonds, hydrophobic core.
77
What is a chaperone and what role do they play?
proteins that assist i folding/ unfoldong and the assembly/disassembly
78
What factors can lead to protein unfolding?̄̉
weakening of non-covalent interactions
79
Give examples of diseases associated with protein unfolding
``` BSE CJD Kuru Alzeimers disease Type 2 diabetes ```
80
What is the main role of myoglobin?
facilitates release of oxygen to the muscle
81
What is the main role of haemoglobin?
Transferring oxygen from lungs to tissues through the blood
82
What are the major components of myoglobin or haemoglobin molecule?
> 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
What is a haem group and what are its properties?
Binding of oxygen to the Fe2+
84
How many subunits make up myoglobin vs haemoglobin?
Myoglobin: > Monomer Haemoglobin: > tetramer
85
What secondary structure dominates the globin protein?
8 a-helices A-H and connecting loops
86
Fe2+ has 6 coordination bind sites, what binds to each of these sites?
4 to nitrogen of haem 1 to nitrogen of histidine F8 of the globin 1 to the 02
87
What is the role of His E7 myoglobin?
Distorts binding of gas molecules to 6th coordination position on haem Fe2+
88
Myoglobin is O2 saturated at low/high pO2 and realeases O2 at low/high pO2
low | low
89
Describe the alternate side-chain packing in R- and T-state haemoglobin
T-State: deoxyhaemoglobin | R-state: oxyhaemoglobin
90
What is an allosteric regulator?
modulating the activity of a protein by the binding of a ligand, called an effector, to an active site
91
Haemoglobin is under allosteric control by which molecule?
BPG
92
How does the compound BPG modify the O2 binding characteristics of haemoglobin?
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
Whys is the O2 saturation curve for haemoglobin sigmoidal?
The binding of the 1st O is harder than the rest
94
Why does the conformation of haemoglobin change on O2 binding?
Brought closer
95
How does shifting from the R-state to the T-state affect how globin interacts with the haem molecule?
increases coopertivity
96
Name 2 factors, other than the allosteric regulator, that facilitate the release of O2
CO2 and H+
97
What is the Bohr effect?
hemoglobin's lower affinity for oxygen secondary to increases in the partial pressure of carbon dioxide and/or decreased blood pH
98
How are the oxygen binding properties of foetal haemoglobin different to that in adult haemoglobin?
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
In what state is the Fe atom in methemoglobin? Does this lead to any effect in regards to haemoglobin's ability to bind oxygen?
Fe3+
100
Will a biological process occur spontaneously if △G>0? Why/why not?
no - requires energy and the substrates dominate.
101
Do enzymes alter the eqbm of a reaction?
Yes
102
What is a transition state in relation to an enzyme catalysed reaction?
Highest energy along the reaction coordinate
103
Does an enzyme bind the substrate to the transition state more tightly?
yes
104
How is the progression of a reaction through the transition state affected by the presence of an enzyme?
The transitions state will have decreased as the activation energy has decreased
105
What are the 2 models used to describe enzyme-substrate binding?
Lock and Key and Induced-fit model
106
How are these 2 models different/similar to each other
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
Why do we need a formal classification system for enzymes?
be able to show the properties of the substrates
108
What types of bonds might we find between an enzyme and substrate?
> Ionic bonds > Hydrogen bonds > Van der Waals Interactions > Covalent bonds
109
How is △Gº⇞ lowered?
1. Ground state destabilisation 2. Transition state stabilisation 3. Alternate reaction pathway with a different transition state
110
What is a cofactor, and what purpose do they serve?
confer specific abilities
111
What is a coenzyme and how it derived?
Small organic molecules, co-substrates, carriers and often derived form vitamins
112
How do coenzymes aid in enzymatic reactions?
Turning substrates into products
113
Why are proximity and orientation effect so vital in enzymatic catalysis?
they have to be close together and in the right orientation or the reaction will not occur.
114
What is covalent catalysis?
Formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme
115
What are electrophiles and nucleophiles and what form of catalysis are they involved in?
nucleophiles donate an electron pair whereas electrophiles accept electron pairs. They drive covalent catalysis.
116
What type of amino acids are likely to be involved in acid-base catalysis?
Glu, Asp | Lys, Arg
117
Covalent catalysis involves the formation of what kind of intermediate interaction with the enzyme?
tetrahedral
118
What is a protease, and what is the difference between a serine protease and an aspartate protease?
proteases break the peptide binds of proteins.
119
What are the important amino acid residues in the active site of chymotrypsin?
Serine superimposes backbone whereas chymotrypsin does not
120
The active site of chymotrypsin contains an oxyanion hole and a specifity pocket. what are these and why are they important?
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
Briefly outline the catalytic mechanism of chrymotrypsin
> nucleophilic attack and covalent catalysis | > Stabilised transition state at the end of the 1st half reaction

Biochemistry (3 decks)

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