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Exam 1 Flashcards

1
Q

What do we have to do to proteins in order to study them?

A

Have to isolate them by size, sequence or charge and purify them

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2
Q

What does SDS-PAGE stand for?

A

Sodium dodecyl sulfate- polyacrylamide gel electrophoresis

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3
Q

Why is polyacrylamide used as opposed to agarose?

A

Has a smaller pore size that is able to capture proteins

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4
Q

What is the charge of the SDS-PAGE gel?

A

Negative- top
positive- bottom

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5
Q

What does SDS-PAGE sort proteins by?

A

Mass! The smaller the protein the farther the migration in the gel

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6
Q

What does SDS do?

A

Breaks non-covalent interactions within proteins to unfold them and coat them with a uniform negative charge

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7
Q

Why are reductants sometimes used in SDS-PAGE?

A

To break covalent disulfide bonds

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8
Q

How does isoelectric focusing gels sort proteins?

A

by pH, when pH=pI, proteins stop migrating

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9
Q

How are charges arranged in an isoelectric gel?

A

From negative to positive

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10
Q

What two methods does 2D gel electrophoresis combine?

A

Isoelectric gel than is then turned sideways and ran through SDS-PAGE gel

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11
Q

What does 2D gel electrophoresis sort proteins by?

A

Size and charge (pI)!

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12
Q

How does the x and y axis decrease for 2D GE?

A

To the right and down!

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13
Q

What proteins absorb light?

A

Aromatic proteins- tryptophan, tyrosine, phenylalanine

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14
Q

What is the UV range for the aromatic proteins?

A

275nm-280nm

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15
Q

Which letters do you look for to indicate light absorption in a protein?

A

W,Y,F

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16
Q

What does Fractionation entail?

A

Also called salting out, the salt concentration is raised which decreases the solubility of certain proteins and produces precipitates

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17
Q

What is the mobile phase of Column Chromatography?

A

Buffer used to wash over the column

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18
Q

Stationary Phase?

A

the column, a solid matrix, functionalized to interact and bind to proteins that usually contain certain properties

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19
Q

What is the Eluate?

A

Buffer/ protein coming off the column

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20
Q

Why is a UV lamp used in column chromatography?

A

Proteins eluded from the column are detected by UV absorbance

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21
Q

How does Ion Exchange Chromatography work?

A

It purifies proteins based on charge. Column named for the type of ion it attracts!!!!! Not the charge of the bead

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22
Q

Why do the proteins bind to the column in a low salt buffer?

A

So the salt ions do not compete with the proteins when binding

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23
Q

How is elute pushed down the column?

A

Salt gradients! Less tightly bound proteins run off first, and more tightly bound proteins go last, requiring a high salt concentration

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24
Q

What is flowthrough, and what is the charge?

A

Flowthrough is the proteins in the mixture that do not bind or interact with the column stationary phase. These proteins will be neutral or the same charge as the column.

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25
How does Gel filtration Chromatography work?
It separates proteins by size. Large molecules elute first because smaller proteins get stuck in the bead pores.
26
How does Affinity Chromatography work?
The stationary phase has immobilized ligands that the protein of interest will want to bind to. Then a mobile phase is added that contain molecules that compete with the protein of interest for binding.
27
What are the characteristics of an amino acid?
A carboxyl group, and amino group, can contain an R-group
28
Where is the alpha carbon in an amino acid?
The first carbon connected to the carbon of the carboxyl group
29
How do we determine what time of amino acid it is?
Based on where the amino group is located in related to the alpha carbon
30
What are the three aromatic amino acids?
Phenylalanine, tyrosine, and tryptophan
31
What species can participate in cation-pi interactions?
aromatic amino acids and positively charged amino acids
32
How does a cation-pi rank in terms of strength?
It is similar to an H-bond!
33
What is pk1?
It describes the ionization of the backbone COOH. usually around 2
34
What is pk2?
Describes the ionization of the backbone amine group, usually around 9
35
What is pkr?
this applies to the functional group side change and is variable
36
Are pk1, pk2, and pkr, dependent opn their surroundings?
Yes!
37
What is the difference between a pka and pI?
Pka relations to a single functional group while pI relates to an entire protein, they are not the same thing!
38
What is zwitterion?
Has a net charge of 0
39
How are amino acids linked together?
A covalent peptide bond that forms a link between the amine and carboxylic acid groups of differing amino acids
40
What are disulfide bonds?
Specialized covalent bonds that aoccur between cysteine residues (the SH), also can play a role in folding of a protein
41
What are some examples of protein modifications?
Phosphorylation, a phosphate is added via a kinase, and removed via a phosphotase
42
Why are modifications important for proteins?
protein structure, non-covalent interactions, and function
43
What does chirality mean?
A carbon is bonded to 4 different substituents
44
What is an enantiomer and why are they important?
A non-imposable mirror image of a molecule. They rotate polarized light differently. Sometimes different enantiomers can opposing or negative effects like in medicine
45
What is a racemic mixture?
An equimolar mixture of enantiomers that does not rotate polarized light
46
Which is a stronger bond, covalent or non-covalent?
Covalent! Involves a sharing of electrons, while non-covalent interactions are more due to electronegativity and polarity
47
Rank non-covalent interactions
ionic, h-bond, dipole-dipole, london dispersion
48
What is involved in an H-bond?
Donor- an electronegative atom bonded to an H atom Acceptor- another electronegative atom with at least one pair of electrons
49
What is the strongest orientation from an H-bond?
When the D-H-A atoms are aligned
50
Why are non-covalent ineractions important?
They stabilize the overall structure of molecules, they facilitate the binding of ligands, and also play a role in solubility
51
What are the differences between conformation and configuration?
Conformation is just the way atoms are related and only requires the rotation of bonds. Configuration is how the atoms are arranged and does require the breaking of bonds.
52
What molecules dissolve well in water?
Charged and polar solutes?
53
What molecules can be absorbed through a membrane?
Small, nonpolar, uncharged molecules
54
Why is dissolving polar or charged molecules favorable in water?
The non-covalent interactions formed between the water and the molecules are energetically favorable
55
What happens when a non-covalent molecule is dissolved in water?
There are little interactions between the molecule and water, rather, water orders itself around the molecule, forming h-bonds between itself, forms a cage
56
What is the hydrophobic effect?
The tendency of hydrophobic molecules to pack tightly together away from water. This packing together reduces number of water molecules forming those cages, freeing up water molecules which increases the entropy.
57
What is an amphiphile?
A molecule that has both hydrophobic and hydrophilic tendencies
58
At pH=pka, what is the ratio of acid to base?
a 50:50 mixture
59
What bond links nucleic acids together to form nucleotides?
phosphodiester bonds
60
How are sugars linked together?
glycosidic bonds
61
What type of reactions to biomolecules participate in and how are they facilitated?
chemical reactions via functional group
62
Are condensation and hydrolysis reactions reversible?
Yes! They are reactions that are at equilibrium
63
Is Keq constant for a reaction in equilibrium?
Yes! While the reaction can go both forward and backward, the net change in products and reactants does not change
64
What does Keq>1 mean?
The reaction is forward dominated in equilibrium, and there is more product than reactant
65
What does Keq<1 mean?
The reaction favors the reverse in equilibrium and there are more reactants than products
66
What is enthalpy?
The heat content of a system
67
What is entropy?
The dispersion of energy/ measure of disorder in a system
68
How do determine the spontaneity of a process?
Using the combination of enthalpy and entropy
69
What is the favorable sign for enthalpy?
Negative
70
What is the favorable sign for spontineity?
Positive
71
How does chemical coupling work?
An endergonic reaction (needs heat) can be coupled with an exergonic reaction through a common intermediate
72
What is an example chemical coupling?
ATP Hydrolysis, many biological reactions are coupled with ATP in order to occur

BMB 401 (3 decks)

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