Brainscape's Knowledge GenomeTM

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


See full index

BIOC192 > Proteins > Flashcards

Proteins Flashcards

1
Q

What are the three main questions biochemists ask?

A

How do cells sense and respond to their environments?
How do cells make and break molecules?
How do cells access and use the energy in food?

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

Name the four interactions between amino acids that stabilise a protein’s tertiary structure.

A

Ionic bond (including metal ion coordination)
Hydrogen bond
Hydrophobic interaction
Disulfide bridge

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

How do cells form polymers (in general)?

A

Dehydration reaction

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

How do cells break polymers down (in general)?

A

Hydrolysis reaction

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

Describe a protein.

A

A non-branching polymer of a specific sequence of amino acids joined by peptide bonds.

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

How large are the macromolecules that proteins form?

A

50-100 Angstroms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Name three methods of determining proteins.

A

Protein crystallography
Electron cryo-microscopy
NMR spectroscopy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Give an example of a protein involved in cell signalling, and how it functions.

A

Insulin- signals cells to take up glucose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Give two examples of proteins involved in digestion, and how they function.

A

Trypsin- breaks down proteins

Amylase- breaks down starch into sugars

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What does HIV Protease do?

A

Breaks down proteins in HIV viruses- essential for replication. Can be made non-functional by using a bound inhibitor.

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

Give two examples of proteins involved in metabolism, and how they function.

A

Alcohol dehydrogenase- helps metabolise ethanol

Hexokinase- helps metabolise glucose by adding a phosphate group to keep it in the cell

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

Give an example of a protein involved in oxygen transport, and how it functions.

A

Haemoglobin- binds oxygen in the lungs and carries it to tissues for use in metabolism

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

How does SARS-CoV2 infect a host cell?

A

Spike protein unfolds and binds to the ACE2 receptor, which triggers fusion of the virus membrane with the epithelial cell membrane.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the central carbon in the amino acid called?

A

Alpha carbon

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

Which is the more predominant enantiomer of amino acid? How is it organised?

A

L-form

CORN (CO at left, R at top and N at right, with H pointing out of the page)

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

How do amino acids exist in solution?

A

Zwitterionic form- the NH2 accepts a proton (NH3+) and the COOH loses a proton (COO-)

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

Which part of an amino acid carries out biochemical reactions?

A

Side chain

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

What is one way of classing amino acids into four groups?

A

Nonpolar amino acids (10)
Uncharged polar amino acids (4)
Negatively charged/ acidic amino acids (2)
Positively charged/ basic amino acids (3)

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

What types of side chains do non-polar amino acids have?

A
  • just hydrocarbon chains (aliphatic)
  • ones containing sulfur
  • rings with no polar group or available N attached
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What characteristics do aliphatic side chains give an amino acid, and how do they help it?

A

Oily ‘patch’

They will be buried inside a protein because they are hydrophobic- this stabilises protein structure.

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

Name the amino acid with a side chain just consisting of hydrogen. What are some of its characteristics?

A

Glycine

It is non-chiral, and flexible because it’s small- so is commonly found in loops of a protein and in connective tissue.

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

Where is cysteine often found and why?

A

In proteases, because it has a sulfhydryl group (SH) in its side chain which is often required for the metabolism of proteins.

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

What is characteristic of phenylalanine and tryptophan amino acids?

A

They both have side chains containing aromatic rings- they are hydrophobic.

  • bulky
  • they have resonance, so ability to fluoresce
  • used to determine concentration of proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is special about proline amino acid?

A

The side chain forms a closed ring, connecting to the amino group- this gives rigidity to protein.

Technically it’s an imino acid because it now contains a secondary amine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What type of side chain do negatively charged/ acidic amino acids have? And why are they termed acidic?

A

One containing carboxyl group COO-

They are displayed in their conjugate base form, so they were an acid that was deprotonated.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What type of side chain do positively charged/ basic amino acids have? And why are they termed basic?

A

One containing a positively charged amine (NH, NH2, NH3)

They are displayed in their conjugate acid form, so they were a base that was protonated.

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

Where are charged amino acids situated in a protein?

A

On the surface, interacting with water- stabilises protein structure.

Or they might be tied up in a salt link with an oppositely-charged residue (electrostatic link).

Or it could be buried within the protein at the active site.

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

What type of side chain do uncharged polar amino acids have?

A

One containing a hydroxyl group (OH) or amide group (O=C-NH2)

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

What are one letter abbreviations of amino acids useful for?

A

Sequence alignment and mutations.

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

What does E6V mean, when describing a mutation?

A

There is a mutation of a glutamate to a valine at position 6 in the protein.

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

What enzyme is RT?

A

Reverse transcriptase, which helps replicate the viral genome in the HIV virus.

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

What is the pKa value for an ionisable group on an amino acid (or protein)?

A

The pH at which the ionisable group is 50% ionised (either protonated or deprotonated).

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

What is the pI of an amino acid (or protein)?

A

The pH at which the net charge is zero- zwitterionic form.

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

Arginine has a pKa of 12.5, what does this mean for its state at biological pH?

A

It is almost always ionised/ protonated.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Histidine has a pKa of 6, what does this mean for its state at biological pH?

A

Roughly half ionised, half not (close to 7.4)

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

What are the pKa’s of the alpha carboxylic acid and amino groups?

A

2

9-10

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

What is the term for protein modification?

A

Post-translational modification

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

How do two (non-adjacent) cysteine amino acids bond?

A

In an oxidising environment, two hydrogens leave and a disulfide bond is formed.

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

Name six amino acid modifications.

A 
Phosphorylation
Hydroxylation
Carboxylation
Metal binding
Iodination
Glycosylation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Describe phosphorylation in terms of proteins.

A

Adding a phosphate (top of side chain) to an enzyme can turn its activity on or off.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Which enzymes can phosphorylate other proteins? How does this work in the case of insulin?

A

Kinases, which are activated when insulin binds to the cell receptor. They activate proteins within the cell that are involved in glucose metabolism.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Describe what hydroxylation of proteins is good for, and which amino acids it involves.

A

Preventing connective tissue diseases and scurvy. Vitamin C is required for hydroxylation. Often proline and lysine are hydroxylated.

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

Describe what carboxylation of proteins is good for, and which amino acid it involves.

A

Blood clotting (essential), glutamate.

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

Which are the most commonly glycosylated amino acids?

A

Threonine and asparagine.

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

Why are proteins glycosylated?

A

Increase solubility

Direct protein to correct binding unit

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

What are people measuring when they take blood sugar?

A

The amount of glycosylated haemoglobin (HbA1c).

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

What are the characteristics of the peptide bond?

A

Planar (due to 40% double character from resonance)
Trans
Partial dipole

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What separates a peptide from a protein?

A

A protein is usually longer and has a defined biological function.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Define amino acid residue.

A

The term an amino acid is referred to as when it’s been bonded with others in a peptide/ protein.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Around which atoms is a peptide chain flexible?

A

The alpha-carbons.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Most proteins are globular, what does this structure require of the peptide chain?

A

To double back and form a compact shape. Primarily composed of alpha-helices, beta-structure and turns.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What is the difference between secondary and tertiary protein structure?

A

Secondary= local 3D arrangement over a short stretch of ADJACENT residues

Tertiary= 3D structure of complete protein chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What is the bond angle between N and alpha-C in the peptide chain?

A

phi Φ angle (anywhere between 0 to +/- 180 degrees)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is the bond angle between alpha-C and C’ in the peptide chain?

A

psi Ψ angle (anywhere between 0 to +/- 180 degrees)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is the peptide bond angle between C’ and N?

A

omega ω (180 degrees- trans, or 0 degrees- cis)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

How can determining the bond angles of a protein help us as scientists?

A

We can use them to define its 3D structure.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

When the peptide chain is shown as a flat zigzag, what are the main chain angles?

A

All 180 degrees.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

Which type of collision can phi rotation lead to?

A

Oxygen to oxygen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

Which type of collision can psi rotation lead to?

A

Amide to amide (NH to NH)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

Why aren’t all bond angles possible?

A

Steric crowding of Van der Waals nuclei

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

Name the bond angle and arrangement of a trans peptide bond.

A

ω of 180 degrees, alpha-carbons are on opposite sides of chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

Name the bond angle and arrangement of a cis peptide bond.

A

ω of 0 degrees, alpha-carbons are on same side of chain- steric hinderance is increased, so requires more energy to make, less common than trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Describe the shape of an alpha-helix.

A

The main chain of the peptide spirals around a central axis (right-handed spiral- thumb= direction up, fingers= direction of chain).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

What is the order of main chain atoms on a protein?

A

N, alpha-C, C’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

How is an alpha-helix stabilised?

A

By hydrogen bonds- electrostatic interactions- between the slight positive charge on amide hydrogens and the slight negative charge on carbonyl oxygens.

They add 12-28kJ/mol stability.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What is the O-N distance in alpha-helices? Why don’t we measure O-H?

A

~ 2.9 Å (four residues apart- O of n, H of n+4)

Hydrogen atoms are too small to see in X-ray resolution.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

How many residues per turn in an alpha-helix?

A

3.6

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

How far does an alpha-helix rise per turn?

A

5.4 Å

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

Where are the side chains in an alpha helix?

A

Pointing out of the helix.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

What are the phi and psi angles of an alpha helix?

A

Φ ~ -57 degrees

Ψ ~ -47 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

What are helix breakers?

A

Residues that end a helix structure.
Glycine- too flexible
Proline- too rigid, amide tied up in side chain, can’t H-bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

In which direction is the alpha-helix dipole?

A

Positive at N-terminus, negative at C-terminus.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

Define beta-strand.

A

A peptide strand with more extended structure than an alpha-helix. Unstable by itself- charged side chains. Typically contains 6 residues, but may have up to 15.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

How is a beta-pleated sheet formed?

A

Forming hydrogen bonds between (2-10) adjacent beta-strands.

Makes a pleated sheet with right-handed twist.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

Describe parallel and anti-parallel orientation of beta-sheets.

A

Parallel= N-C terminus directions of two beta-strands are the same. Hydrogen bonds are diagonal to strands.

Anti-parallel= N-C terminus directions of two beta-strands are the opposite. Hydrogen bonds are perpendicular to strands. (Lots of this in nature)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

Which stretch of residues typically forms a beta-sheet ?

A

Non-polar, polar alternating. All non-polar side chains stick out above/ below, and all polar side chains stick out below/ above. They can form a structure with another similar sheet and create a non-polar region between them. e.g. silk

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

Describe a turn in protein structure.

A
  • usually 3 or 4 residues where the strand changes direction
  • require flexibility and rigidity- high glycine and proline content
  • involve ~ 30% residues in a chain
  • required to form globules
  • commonly involves a hydrogen bond across the turn
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

Define random coil in protein structure.

A

A stretch of protein structure that doesn’t fit into the standard groups (i.e. turns, helices, sheets).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

Define protein domains.

A

Small proteins/ parts of proteins that can fold independently, and have a specific function within the protein. They can be reused and combined.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

Define supersecondary protein structure.

A

Elements of secondary structure connected by turns or coils. (protein subdomains)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

Name four common motifs of supersecondary protein structure.

A

Helix-turn-helix
Beta hairpin
Greek key
Strand-helix-strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

Give two examples of proteins that include helix-turn-helix supersecondary structure.

A

DNA binding proteins

Calcium binding proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

Describe beta-hairpin supersecondary structure and name two proteins that include it.

A

Two antiparallel beta-strands connected by a turn and H-bonds. Very common motif, of varying lengths.

Bovine pancreatic trypsin inhibitor
Snake venom toxin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

Describe Greek key supersecondary structure.

A

Four antiparallel beta-strands- basically one long, bent over hairpin.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

Describe strand-helix-strand supersecondary structure.

A

Beta-strand then a turn then a helix then a beta-strand. The strands are on the same plane (with the helix slightly above), so can stabilise each other via hydrogen bonds. Favourable interactions can occur between the side chains of the helix (pointing out) and the side chains of the strands (pointing up).

Very common motif.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

Which component of a typical protein domain is very important for stability?

A

A hydrophobic core.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

What are three families of tertiary structure that proteins can be grouped into?

A

Alpha domain family
Alpha/ beta family
Antiparallel beta family

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

Name two subgroups within the alpha domain family.

A

Four helix bundle

Globin fold

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

Describe the four helix bundle tertiary structure.

A

Four alpha-helices tilted slightly to each other, in sequence. The tilting allows the side chains to pack more tightly. (helix, turn, helix, turn, helix, turn, helix, turn)

Hydrophobic core consists of oily residue side chains between the helices. The outsides of the helices have hydrophilic side chains. This means the helices are amphipathic.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

Describe the globin fold tertiary structure.

A

Amphipathic helices with side-chains packed closely together within a hydrophobic core. But- unlike the four helix bundle- packing can occur between non-adjacent helices.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

Name two subgroups within the alpha/beta family.

A

Alpha/ beta barrel

Alpha/ beta horseshoe fold

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

Describe the alpha/ beta barrel structure.

A

Helix, turn, strand, turn, helix, turn, strand, turn, etc.
Strands circle inside helix circle and form a hydrophobic barrel core. Side chains at the top of the barrel are hydrophilic and point out into the solution- often the active site of an enzyme.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

Describe the alpha/ beta horseshoe fold.

A

16 strand, helix motif repeats creating a horseshoe shape.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

Name one subgroup within the anti-parallel beta family.

A

Anti-parallel beta barrel.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

Describe the anti-parallel beta barrel structure, and one protein that has this structure.

A

Strand, turn, strand, turn etc.
Loop around to form a barrel with hydrophobic core. Present in antibodies and surface antigens.

Retinal binding protein is an anti-parallel beta structure. The retinal binds in the hydrophobic core, but has an OH hydrophilic group that sticks out the bottom.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

What was biochemist Christian Afinsen’s famous finding?

A

The amino acid sequence contains all the instructions required for the folding of the protein.

97
Q

What is the likely sequence of events in protein folding?

A

(dictated by the need to build a hydrophobic core)

  1. Short secondary structure segments form
  2. Subdomains/ supersecondary structures form
  3. Subdomains/ supersecondary structures come together to form a partly folded protein/ ‘molten globule’ that can rearrange
  4. Final domain structure emerges
98
Q

How do chaperone-dependent and chaperonin-dependent proteins fold?

A

Chaperone-dependent proteins require proteins that bind and assist temporarily (chaperones- e.g. Hsp70) to prevent the oily structures from aggregating.

Chaperonin-dependent proteins require chaperones, and a chaperonin protein (e.g. GroEL-GroES) that acts like a bin which the protein goes inside and ATP is used to fold it.

99
Q

What are some examples of things that might denature a protein?

A 
Change in pH (irreversible)
Heat (irreversible)
Detergents
Organic solvents
Urea
Guanidium
100
Q

What is PrP, and what three conditions can it cause?

A

A prion protein that changes shape/ misfolds (alpha to beta), then promotes other proteins to misfold. This spreads and the prions aggregate to form plaques and tangles that destroy brain function.

Bovine spongiform encephalopathy (BSE)- eating beef that’s contaminated with prions
Creutzfeld-Jacob disease (CJD)- receiving pituitary transplant of someone with prions
Kuru- ingesting human brain

101
Q

Which two diseases do misfolded proteins (but not prions) contribute to?

A

Alzheimer’s disease
Type 2 diabetes

Amyloid (type of misfolded protein) plaques can develop in the brain.

102
Q

What is the concentration of haemoglobin in the blood?

A

~5 mmol/L

103
Q

Describe the function of myoglobin.

A

Stores oxygen in muscles for use during intense exercise.

104
Q

How do haemoglobin and myoglobin relate to evolution?

A

There is a strong evolutionary pressure for efficient oxygen delivery. The more oxygen you can get to your muscles, the faster and further you can run.

105
Q

How much myoglobin do humans have?

A

0.5-0.7 mmol/L

106
Q

Describe the structure of myoglobin.

A

Primary: ~150 amino acids
Secondary: 8 alpha-helices labelled A-H, connecting loops labelled AB, BC etc.
Tertiary: globin fold with a hydrophobic pocket, where a haem group is binded by His F8
Quaternary: monomeric

107
Q

How are amino acids numbered in myoglobin and haemoglobin?

A

First, the letter of the helix they are present on, and second, their position within that helix. e.g. F8

108
Q

Describe the structure of a haem.

A

A protoporphyrin, comprised of four pyrrole rings (of 4 carbons and a nitrogen) in a plane. Between the four nitrogens, the iron atom is held.

109
Q

How is the haem bonded to the myoglobin?

A

The iron atom has six coordinate bonds to ligands:

  • 4 to the nitrogen atoms of the haem
  • 1 to histadine F8 of the globen
  • 1 to O2 molecule
110
Q

Why does the protoporphyrin (haem) have a red colour?

A

It has absorbance in the visible light spectrum because it has a huge molecular orbital due to conjugation between double bonds.

111
Q

What will change the molecular orbital of haem, and what effect will this have? How can we see this effect?

A

Whether oxygen is bound or not (O is electron-rich), and the blood colour changes- duller red if no O2.

We can use spectroscopy- shine particular colour of light, and see if it absorbs it- allows us to identify compounds.

112
Q

Why is the O2 bound by His E7 at an angle?

A

It is less stable in this position, which reduces the binding affinity of oxygen to myoglobin, so it’s easier to release into the cell.

113
Q

Why doesn’t haem travel naked in the blood?

A

Without the histadine in the way, the oxygen would bind strongly to the iron atom, and would never be released.

114
Q

Define allosteric control, and give an example involving myoglobin.

A

Controlling a protein’s function ‘without overlapping’.

Lactate (anion of lactic acid) decreases myoglobin’s affinity for oxygen, but does not bind where oxygen binds. This promotes oxygen release from myoglobin.

115
Q

What does the availability of O2 to cellular proteins depend on?

A
  • pO2 in the local environment

- binding affinity of O2 to haemoglobin

116
Q

How do myoglobin and haemoglobin differ in O2 binding?

A
  • myoglobin has a hyperbolic curve= only releases O2 (low saturation) when pO2 is very low
  • haemoglobin has a sigmoidal curve, for cooperativity

Basically, myoglobin has tighter binding to oxygen, and haemoglobin has weaker binding.

117
Q

How does pO2 vary throughout the body?

A

Much higher in the lungs (100 Torr), compared to the muscles (20 Torr). So haemoglobin can pick up a lot of oxygen in the lungs, and drop it off to the muscles.

118
Q

Describe the shape of haemoglobin.

A

Tetramer of two alpha subunits and two beta subunits- all very similar to myoglobin. They interact non-covalently, and each contain a haem and bind one O2.

119
Q

Describe the MWC model of cooperativity.

A

All four subunits of a tetramer must be in the same state- low-activity T tense, or high-activity R relaxed.
Binding each substrate (O2) shifts equilibrium in favour of R state- makes it more likely the tetramer will shift to the R state.

Explains sigmoidal curve of haemoglobin.

120
Q

Describe the KNF sequential model for some enzymes.

A

There are intermediate forms where all four subunits don’t have to be in the same state. Binding substrate makes binding the next easier (or harder- negative cooperativity).

121
Q

Name three main differences between haemoglobin and myoglobin.

A

H transports O2, M stores O2.
H is a tetramer, M is a monomer.
M has a tighter-binding hyperbolic curve, H has a weaker-binding sigmoidal curve.

122
Q

Summarise cooperativity in terms of haemoglobin.

A

Binding at one subunit makes binding at the successive subunits easier.

123
Q

Why can’t myoglobin show cooperativity?

A

It’s a monomer- only one binding site.

124
Q

What are the structural differences between deoxyhaemoglobin and haemoglobin?

A

In deoxyhaemoglobin, the F helix is risen, which pulls the haem upwards and giving it a dished shape. This shape is worse for binding O2.

In oxyhaemoglobin, O2 flattens the haem (pulls the Fe2+ into the plane of the haem), which pulls His F8 and helix F toward the binding site. This shape is better for binding O2.

125
Q

Define a conformational change. What is an example in haemoglobin?

A

Shifts in the orientation of protein secondary elements.

Helix F moves relative to helix C.

126
Q

How do the T and R states relate to types of haemoglobin?

A

Taut T-state = deoxyhaemoglobin

Relaxed R-state = oxyhaemoglobin

127
Q

How do the subunits of haemoglobin interact?

A

The F-helix of one haem interacts with the C-helix of another- moving from the T-state to the R-state, passing through the unstable intermediate state. Alternative interactions stabilise each state.

Moving into the R-state is its way of communicating it has bound an O2.

128
Q

Describe BPG and its function within haemoglobin.

A

2,3-biphosphoglycerate is an allosteric inhibitor of O2 binding to haemoglobin. It is highly negatively charged, so can bind to the positive side chains (histadines and lysines) of the haemoglobin at the allosteric site- in the middle of the four subunits.

This electrostatic interaction stabilises the T state, reducing O2 affinity and promoting release of O2. BPG is produced during respiration in peripheral tissues when more O2 is needed.

129
Q

What does the sigmoidal binding curve of haemoglobin tell us about its function at different points in the body?

A

The fraction of oxyhaemoglobin is very high at arterial pressure, so it is good at picking up lots of oxygen from the lungs.

The fraction of oxyhaemoglobin drops abruptly at venous pressure, demonstrating how cooperativity allows efficient unloading of O2.

130
Q

Describe two other allosteric inhibitors of O2 binding to haemoglobin.

A

CO2- can bind to the extreme N terminal amino group
H+ (low pH)- can protonate certain amino acid side chains e.g. histidine

Both of these contribute to stabilising the deoxy-Hb conformation.

131
Q

What occurs in haemoglobin at high altitudes?

A

Reduction in oxygen binding due to an increase in BPG. Allows oxygen to deliver more O2 to tissues.

132
Q

How does foetal haemoglobin differ from adult haemoglobin?

A

It includes alternate isoforms, e.g. gamma, that have higher affinities for O2. This allows the foetus to capture O2 from the mother’s blood across the placenta.

They also lack an amino acid at the BPG binding site, so bind BPG less well than adults.

133
Q

At high altitudes, how do the mother and foetus continue delivering enough O2 to their tissues?

A

The mother’s haemoglobin binding affinity drops significantly more than the foetus’s, because the foetus can’t bind BPG as well. BPG makes releasing O2 to the tissues easier.

134
Q

Describe methaemoglobin.

A

Damaged haemoglobin in which the haem is oxidised from Fe2+ to Fe3+, which shifts one subunit to the R-state without having oxygen bound.

This keeps the other subunits in the R-state (cooperativity), so they don’t release O2 into the tissues.

135
Q

Describe Boston haemoglobin.

A

Haemoglobin with a H58Y mutation, or a His E7 mutation to Tyr E7. This causes Fe2+ to oxidise to Fe3+. The haem plane moves slightly, breaking the connection of Fe to His F8.

This stabilises the T-state, with low affinity for oxygen.

136
Q

Describe sickle cell haemoglobin.

A

Haemoglobin with an E6V gain of function mutation. The valine binds really well to the hydrophobic pocket of another tetramer. These tetramers tack up and cause a deformed cell shape- can get stuck in capillaries.

137
Q

Define enzymes and their function.

A

A biological molecule that catalyses (increases the rate of) a chemical reaction. Most enzymes are proteins- some are RNA’s (ribozymes).

138
Q

How do enzymes increase the rate of a reaction? What remains the same?

A

By lowering the activation energy. They don’t change the free energy of products or reactants, and they don’t change equilibrium.

139
Q

Why do enzymes exist in the body?

A

To enhance specific chemical reactions in the cell and create organisation.

140
Q

What does a negative Gibbs energy suggest?

A

Products dominate at equilibrium, energy is released, the reaction is favourable.

141
Q

What does a positive Gibbs energy suggest?

A

Substrates dominate at equilibrium, energy is required, the reaction is unfavourable.

142
Q

What does ΔG°‡ determine?

A

Activation energy (needed to reach transition state) determines the rate of reaction. The higher the activation energy, the slower the reaction.

143
Q

What do aldolase and adenylate kinase have in common?

A

Enhance the reactions rates of unfavourable reactions.

144
Q

Define isozymes.

A

Enzymes that catalyse the same reaction, but differ in sequence.

145
Q

Define oxidoreductases.

A

A class of enzyme that catalyses redox reactions.

146
Q

Define transferases.

A

A class of enzyme that catalyses reactions involving a transfer of a functional group.

147
Q

Define hydrolases.

A

A class of enzyme that catalyses hydrolysis reactions.

148
Q

Define lyases.

A

A class of enzyme that catalyses reactions that involve making/ breaking bonds without using H2O.

149
Q

Define isomerases.

A

A class of enzyme that catalyses reactions that transfer atoms/groups within a molecule to produce an isomer.

150
Q

Define ligases.

A

A class of enzyme that catalyses reactions that forms a bond between two molecules, usually coupled to ATP cleavage.

151
Q

Name two ATP hydrolyases.

A

Myosin (in muscle), and ATP synthase.

152
Q

Describe the properties of the active site on an enzyme.

A
  • has amino acid side chains projecting into it
  • binds the substrate via weak interactions
  • determines the specificity of the reaction (how many substrates can it bind)
153
Q

Name the types of enzyme-substrate bonds.

A

Ionic bonds- make use of charged side chains
Hydrogen bonds- good for specificity
van der Waals interactions- between any enzyme and substrate atoms in close proximity
Covalent bonds- rare, much stronger bonds

154
Q

Describe the two models for enzyme-substrate binding.

A

Lock-and-key model (Fischer)- the active site is already the perfect fit for the substrate

Induced-fit model (Koshland)- the active site undergoes conformational change when it binds the substrate

155
Q

Why are weak bonds used in enzyme-substrate binding?

A

They allow reversible binding- release of the substrate. If the bond is too strong, the Gibbs energy of enzyme-substrate complex is too low, and the activation energy is higher.

They also ensure specificity.

156
Q

How do enzymes lower activation energy?

A

Ground state destabilisation
Transition state stabilisation- complementary to transition state
Alternate reaction pathway- lower energy transition state

157
Q

Describe cofactors.

A

Can be organic (coenzymes) or inorganic (metal ions).
Position the substrate in the correct geometric and chemical orientation at the binding site of the enzyme.
Small molecules that carry an electron, atom or functional group.
Many coenzymes derived from vitamins (B).

158
Q

Name 6 strategies by which enzymes drive catalysis.

A 
Acid-base catalysis
Covalent catalysis
Redox and radical catalysis
Geometric effects
Stabilisation of transition state
Cofactors with activated groups
159
Q

How many catalysis strategies do enzymes use?

A

Many use more than one.

160
Q

What often drives redox catalysis?

A

Metal ions

161
Q

Describe covalent catalysis.

A

Nucleophilic side chain of enzyme cleaves the substrate bond to form a reactive, short-lived intermediate, which is covalently attached to the enzyme. Another reaction- often hydrolysis- is required to remove the substrate from the enzyme.

162
Q

Name two geometric effects that can catalyse a reaction.

A

Proximity and orientation.

163
Q

Name four good nucleophiles.

A

RÖ:- (Hydroxyl group)
RS̈:- (Sulfhydryl group)
RN̈H2 (Amino group)
Imidazole group

164
Q

What drives covalent catalysis?

A

Nucleophilic attack

165
Q

What does almost every reaction that involves breaking a phosphate use?

A

Magnesium or manganese as a cofactor

166
Q

How does Mg2+ catalyse the cleavage of a phosphate bond?

A

Establishes orientation of phosphates

Stabilises negative charge on oxygens of two adjacent phosphates, making them better leaving groups and electrophiles.

167
Q

What does acid-base catalysis involve?

A

Ionisable groups, in the correct ionisation state, and proton transfer.

168
Q

Explain how enzyme activity is pH dependent.

A

Each enzyme has a characteristic optimal pH at which its rate is highest, because the amino acid side chains need to be in the correct ionisation state for the catalytic mechanism to proceed.

169
Q

Which amino acid is particularly suitable to acid-base reactions, and why?

A

Histidine, because its side chain (an imidazole) has a pH of 6.5. This means it can easily accept and donate a proton at physiological pH.

170
Q

Name some properties of chymotrypsin.

A

Since it’s a protease:

  • hydrolyase
  • polypeptide and H2O substrates
  • two shorter peptides or amino acids products

Chymotrypsin acts in digestion.

171
Q

Name three serine proteases and how they are related.

A

Chymotrypsin
Trypsin
Elastase

Related through divergent evolution.

172
Q

What is the difference between divergent and convergent evolution?

A

Divergent- have a common ancestor, and diverge (same structure, unique specificities)
Convergent- no common ancestor, but shared traits (different structure)

173
Q

What two features do serine proteases share?

A

Catalytic triad- Aspartate, Histidine, Serine

Specificity pocket- governs where the protein will be cleaved

174
Q

What is the scissile bond of a protein, and how does the enzyme decide where to cut? Give examples for three serine proteases.

A

The bond to be cleaved.

The side chain next to the scissile bond sits in the specificity pocket of the enzyme.

Chymotrypsin- contains two glycines, so there’s a lot of space for a large side chain
Trypsin- contains a negative aspartate, so only cleaves next to a positive side chain
Elastase- valine and threonine fill pocket, so only has room for small side chains

175
Q

How can we tell subtilisin and chymotrypsin are related through convergent evolution?

A

Their peptide backbones do not superimpose- different structures. The same catalytic triad occurs, but not in the same order and structure.

176
Q

How can we tell the catalytic triad is a very effective mechanism?

A

Evolution has found it through different ancestry routes.

177
Q

Which catalytic mechanisms are used in chymotrypsin catalysis?

A 
Geometric effects (proximity + orientation)
Covalent catalysis (nucleophilic attack + stabilisation of transition state)
Acid-base catalysis (moving a proton)
178
Q

Where does the covalent bond from in chymotrypsin catalysis?

A

Between O of serine and alpha-C of peptide

179
Q

What does a progress curve display? (enzyme)

A

The appearance of product/ disappearance of substrate over time.

180
Q

What feature of an enzyme catalysed reaction do we usually measure?

A

The initial reaction velocity, Vi or Vo

181
Q

How does the initial rate Vi change with increasing concentration of substrate [S]?

A

Increases linearly at first
As all the enzyme sites are occupied, the rate of reaction stops increasing- since we aren’t increasing the number of enzymes, there’s

182
Q

Define Vmax on a V vs [S] curve.

A

Maximum possible velocity (when [S]=0. The asymptote that the curve approaches, but never reaches.

183
Q

Define KM on a V vs [S] curve.

A

Michaeli’s constant- the [S] at which V=Vmax/2

The smaller the KM, the better the enzyme is at binding substrate.

184
Q

Describe simple enzyme catalysis in terms of E, S, P, k1, k-1, and k2.

A

Enzyme, E, converts a substrate, S, into a product, P.
It first has to bind the substrate: enzyme-substrate complex.
k1 and k-1 are the rates of the forward and reverse reactions of the substrate binding/ releasing
k2 is the rate of catalysis- relates to activation energy required to reach transition state

185
Q

Define the Michaelis-Menten equation.

A

V = (Vmax [S]) / (KM + [S])

Describes the shape of the V vs. [S] curve

186
Q

Name the five assumptions of the Michaelis-Menten equation.

A
  • product is not converted back into substrate
  • [S]&raquo_space; [E]
  • ES steady state (formation and breakdown rates of ES complex are equal)
  • [S] does not change significantly (why we use initial V)
  • all ES complexes have the same reaction rate
187
Q

Which enzymes violate the Michaelis-Menten curve? Why do we need these?

A

Cooperative and allosteric enzymes. To act as control points in metabolic pathways.

188
Q

How do cooperative enzymes violate the Michaelis-Menten curve?

A

Their V vs. [S] plot is sigmoidal, not hyperbolic, because cooperativity of subunits ensures they respond more steeply to intermediate changes in [S].

189
Q

How does phosphofructokinase fulfill and violate the Michaelis-Menten curve?

A

With no allosteric inhibitors - hyperbolic curve. This happens at low ATP because we need to perform glycolysis to produce ATP.

With allosteric inhibitors (ATP or PEP) - sigmoidal curve. high ATP pushes enzyme into T state where it’s much less active.

Cooperative behaviour

190
Q

Describe the transition between T and R states in phosphofructokinase.

A

Positively charged Arg side chain binds substrate via electrostatic interaction. Loop flips to bring negatively charged Glu side chain into binding site, which repels the negatively charged substrate.

191
Q

What does k-1 [ES] + k2 [ES} = k1 [E] [S] show?

A

Steady state assumption- that the rate of enzyme-substrate complex formation= rate of its breakdown

192
Q

Describe the Lineweaver-Burk plot, and what the x and y intercepts mean.

A

The reciprocal of max velocity vs. the reciprocal of substrate concentration. (enzyme-catalysed reaction)

x-intercept= -1/KM
y-intercept= 1/Vmax
193
Q

A more negative x-intercept on a Lineweaver-Burk plot shows what?

A

A large -1/KM = a small KM = high affinity for substrate.

194
Q

KM = k-1 / k1

Explain the formula and the assumption made.

A

KM describes the binding of substrate to enzyme. It depends on the formation of ES (k1) and the breakdown of ES (k-1 and k2).

Technically, KM = (k-1 + k2) / k1
But, since the breakdown of ES to form E + P (k2) is very slow compared to the equilibrium step between E + S and ES. Since the reaction is slow, k2 is very small, and negligible- k2 &laquo_space;k-1

195
Q

How do enzymes maintain steady state in the body?

A

They will adjust their rate to keep their KM in the physiological range of [S].

196
Q

When might an enzyme have two KMs?

A

When it can bind two different substrates.

197
Q

Why does hexokinase have a hyperbolic V vs. [S] curve, while glucokinase has a sigmoidal V vs. [S] curve?

A

Hexokinase binds glucose to produce ATP. This is essential at low energy, so needs a fairly high rate with low glucose concentration.

Glucokinase binds glucose to produce starch. We don’t want glucose being stored away at low glucose concentration, because we need it for energy, but we want to store it at high concentration.

198
Q

Define kcat.

A

The turnover number= the number of substrate molecules converted to product per enzyme per unit of time (when E is saturated with substrate).

199
Q

When does kcat = k2?

A

When the enzyme fits the Michaelis-Menten model.

200
Q

How does kcat describe the rate limiting step? (formula)

A

Vmax = kcat {E}total

201
Q

What does kcat / KM measure? Explain.

A

Enzyme efficiency

A high kcat and a low KM means a fast turnover and a low [S} for max velocity (high binding affinity).

202
Q

Define the enzyme efficiency of a ‘perfect catalyst’.

A

> 10^8 s^-1 M^-1

203
Q

Give an example of a very efficient catalyst.

A

Acetylcholinesterase- breaks down neurotransmitter (ACh) is nerve synapses. Efficiency of 1.5 x 10^8

204
Q

Name four reasons enzyme inhibitors are important.

A

Regulate metabolism
Basis of many drugs and poisons
Used to study enzyme mechanisms
Used to study metabolic pathways

205
Q

Describe the classes and subclasses of enzyme inhibitors.

A

Irreversible= binds covalently to an aa side chain in the active site and deactivates the enzyme
Reversible= binds non-covalently to the enzyme and can be released, leaving the enzyme in its original condition
- competitive= inhibitor competes with substrate for binding at the active site
- non-competitive= inhibitor binds at a different site to the substrate (allosteric)

206
Q

How does TPCK disable chymotrypsin?

A

End group covalently binds to the histidine of the catalytic triad, disabling it and filling the active site with its bulkiness. This blocks substrate binding.

207
Q

What changes in competitive inhibition- Vmax or KM? Why?

A

KM increase, because more substrate is needed to get V up to half of Vmax (= KM).

Vmax doesn’t change, because V can still be really high if [S]&raquo_space; [inhibitor]. Most enzymes will bind the substrate instead of the inhibitor.

208
Q

Define transition state analogues.

A

A class of competitive inhibitor that has the structure very similar to that of the transition state (between S and P). It will bind very well to the enzyme at the active site, but the reaction can’t proceed- may be due to a bad leaving group.

209
Q

When might a competitive inhibitor that proceeds to react be beneficial?

A

Alcohol dehydrogenase binds both methanol and ethanol. If [methanol] is too high, we can flood the space with ethanol to prevent poisonous formaldehyde from forming, and produce harmless acetaldehyde instead.

210
Q

What changes in pure non-competitive inhibition- Vmax or KM? Why?

A

Vmax decreases, because they’re not competing for the same site, so the inhibitor can decrease the rate.

KM doesn’t change because the binding of inhibitor has no effect on the active site where the substrate binds.

211
Q

Name the four common steps of activation and inhibition of proteins.

A

Chemical substance travels from its source.
Chemical substance binds to target protein.
Binding causes activation/ inhibition of protein.
Activation/ inhibition causes change in cellular response.

212
Q

Define receptor.

A

A cellular protein (or assembly of proteins) that controls chemical signalling between and within cells.

213
Q

How do receptors differ from enzymes?

A 
Can have more than one binding site.
Bind ligands (not substrates).
Release the ligand unchanged (not converted to product).
214
Q

Name the three classes of receptor.

A

Ligand-gated ion channel
G protein coupled receptor GPCR
Receptor tyrosine kinase RTK

215
Q

Define ligand.

A

Chemical substance that specifically binds to a receptor.

216
Q

Define endogenous and exogenous ligands.

A

Endogenous are produced in the body, exogenous are produced outside the body (drugs, poisons).

217
Q

Where are most receptors found? What function do they serve there?

A

On the outer cell membrane, so they can sense changes in the extracellular environment and cause intracellular response.

218
Q

Describe how ligands and receptors show specificity.

A

The size and shape of the ligand must match the corresponding receptor binding pocket. This allows enough chemical interactions for binding to occur.

219
Q

How do medicinal chemists come up with new drugs?

A

They start with the chemical structure of an endogenous ligand, and modify it to make something safe and effective.

220
Q

Define agonist and antagonist (ligands).

A

Agonist is a type of ligand that causes activation of a receptor when it binds.

Antagonist is a type of ligand that binds to a receptor and prevents the agonist from binding. This inhibits the receptor.

221
Q

Describe signal transduction (receptor).

A

Receptor undergoes a conformational change, becoming active and starting a chain of events in which messages are passed through the cell.

222
Q

Define second messengers.

A

Proteins or chemical signals that are free to move in the cell, so can pass on messages on signal transduction.

223
Q

How do GPCRs start signal transduction?

A

Activate the G protein when agonist ligand binds.

224
Q

Name two common G proteins, and their roles.

A

G alpha s (stimulatory protein that activates adenylate cyclase)
G alpha i (inhibitory protein that decreases the activity of adenylate cyclase)

225
Q

How do RTKs start signal transduction?

A

By phosphorylating an adaptor protein when the agonist ligand binds.

226
Q

Which enzymes perform phosphorylation in the cell, and how?

A

Protein kinases transfer phosphates from ATP to protein.

227
Q

Which enzymes perform dephosphorylation in the cell, and how?

A

Protein phosphatases rapidly remove the phosphates from proteins to control signal transduction.

228
Q

Define phosphorylation cascade.

A

A signal transduction pathway that uses many different protein kinases to phosphorylate/ activate the next in sequence, and ultimately activate the protein.

229
Q

What occurs when a ligand-gated ion channel is activated?

A

Ions flow directly through the channel, into the cell, to produce effects. (no second messengers)

230
Q

Name the key difference in performance of ligand-gated ion channels compared to GPCRs and RTKs.

A

Fast signalling

231
Q

What are some factors that can change the response from a receptor?

A

Where on the cell/ body it is expressed.
Different relay molecules.
Pathway branching and cross-talk from other receptors on the cell.

232
Q

What kind of ligand is insulin?

A

Endogenous peptide ligand.

233
Q

On which three cell types does insulin act?

A

Muscle, adipose, liver.

234
Q

How does insulin cause a response in muscle and adipose cells?

A

Activates RTK receptor, which phosphorylates an adaptor protein. This leads to further signal transduction, and finally the transport of GLUT-4 (a glucose transporter) to allow glucose entry into the cell.

235
Q

How does insulin cause a response in liver cells?

A

Activates RTK receptor, which phosphorylates an adaptor protein. Further signal transduction leads to glycogen synthesis.

236
Q

What kind of ligand is glucagon?

A

Endogenous peptide ligand.

237
Q

How does glucagon cause a response in liver cells?

A

Activates GPCR, which activates a stimulatory G protein. Further signal transduction leads to glycogen breakdown.

238
Q

Define GLP-1.

A

An endogenous peptide ligand (hormone) which is produced in the gut, and acts on pancreatic beta cells.

239
Q

How does GLP-1 cause a response in pancreatic beta cells?

A

Activates GPCR, which activates a stimulatory G protein. Further signal transduction leads to insulin secretion.

BIOC192 (3 decks)

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