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Biochemistry > Chapter 4: Protein structures > Flashcards

Chapter 4: Protein structures Flashcards

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1
Q

How many layers do gobular proteins have

A

They will typically have at least 2 layers of 2° structure

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2
Q

Hydrophobicity residue is greater where?

A

It is more likely to be found in the protein’s interior

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3
Q

Myoglobin binds what?

A

Myoglobin binds oxygen in muscles

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4
Q

Proteins are stabilized through what effect?

A

Hydrophobic effect

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5
Q

What type of interactions stabilize proteins

A

Electrostatic or ionic interactions.

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6
Q

What stabilizes extracellular proteins?

A

Disulfide bonds.

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7
Q

What are the different types of ways that stabilize proteins

A

hydrogen bonds, ionic bonds, hydrophobic effect, disulfide bond

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8
Q

In vivio

A

A newly synthesized polypeptide begins to fold as it leaves the ribosome. They sometimes require molecular chaperones ( they prevent mistakes).

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9
Q

In vitro

A

Full length polypeptide is denatured and then allowed to renature. Not random.

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10
Q

What does the hydrophobic effect do to proteins

A

It stabilizes the protein and it drives proteins to fold.

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11
Q

What is the other name of gel-filtration chromatography

A

Also known as size exclusion.

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12
Q

Size-exclusion Chromatography

A

Easy to use. Also known as gel filtration. Separation is based on size

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13
Q

Ion exchange chromatography separates based on what?

A

It is a process for separating proteins in a solution based on differences in net charge.

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14
Q

Composition of proteins

A

Made of one or more polypeptides. Polypeptides are a chain of amino acids.

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15
Q

Composition of proteins

A

Made of one or more polypeptides. Polypeptides are a chain of amino acids.

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16
Q

Amino Acid

A

A small molecule that contains an amino group and a carboxylate group and a side chain that varies in structure known as the R group. At physiological pH the carboxyl group is unprotonated and the amino group is protonated. The amino acid bears both a negative and positive charge.

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17
Q

Classification of R groups

A

They are classified by their overall chemical characteristics: hydrophobic, polar, or charged.

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18
Q

Alpha Acid

A

The amino and carboxylate acid groups are both attached to the central carbon atom that is known as the alpha carbon.

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19
Q

How many chiral amino acids?

A

19 of the 20 are chiral molecules.

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20
Q

In proteins where are hydrophobic amino acids found?

A

They can be located in the inside of the molecule with other hydrophobic groups. They do not interact with water.

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21
Q

Some polar side chains can ionize at physiological pH values. Ex. netural (basic) histidine.

A
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22
Q

Deprotonation of cysteine to yield thiolate anion

A

It can be deportinated outside the cell

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23
Q

Oxidation of Cysteine thiol group.

A

When another thiol group is near by it will form a disulfide bond.

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24
Q

What four amino acids have side chains that are always charged under physiological conditions?

A

Aspartate (Asp), glutamate (Glu); have carboxylate groups that are negatively charged. Lysine (lys) and arginine (Arg) are positively charged.

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25
Are charged amino acids located internally or in the proteins surface?
Amino acids with charged side chains can be found on the surface of the protein.
26
Peptide bond
The amide bond linking two amino acids.
27
pK values of amino acids
Know that carboxylates are around 4 pka. And amino acids range form 9-10.
28
Estimate net charge example.
29
Name for short polypeptides
Oligopeptides or peptides
30
Most proteins contain all 20 amino acids. what is the ave MW of an amino acid
100 Da average mw. Most abundant amino acid is Leu.
31
Amino acid residue
What remaining portion of the amino acid acid from the peptide bond.
32
Condensation reaction
When a water molecule is eliminated. When to amino acids link they do so from the carboxylate group and the amino group. The carboxylate group loses the oxygen and the amino group loses the hydrogens.
33
Which functional group of an amino acid is located on each side of the polypeptide chain?
The N terminus has the amino group. The C terminus has the carboxylate group.
33
Which functional group of an amino acid is located on each side of the polypeptide chain?
The N terminus has the amino group. The C terminus has the carboxylate group.
34
The peptide bond has two resonance forms
Because of the double-bond no rotation is possible around the C-N bond.
35
First level of the protein structure
The sequence of amino acids is known as the primary structure. AKA just the words.
36
Secondary structure
The spatial arrangement of the polypeptide backbone. Under physiological conditions the polypeptides folds.
37
Tertiary structure
The complete 3D conformation of the polypeptide; includes backbone atoms and the side chains.
38
Quaternary structure
A protein that has more than one polypeptide chain. It is the spatial arrangement of the polypeptide chains in a protein with multiple subunits.
39
Alpha helix
The polypeptide backbone twists in a right-handed fashion where the hydrogen bonds form between the carboxylate and amino groups. The hydrogen bonds along the helical axis stabilize it
40
Rotation of N—Cα and Cα—C
The rotation is limited due to steric constraints.
41
Beta sheet
Secondary structure that has aligned strands of polypeptide where the h-bonds are met by bonding to the neighboring strands. They are anti-parallel or parallel.
42
Parallel b sheet
Where the neighboring chains run in the same direction.
43
Anti parallel b sheet
The neighboring chains run in the opposite direction.
44
B strands can be connected by turns and loops.
45
Which type of beta sheet is more stable?
Antiparallel is more stable.
46
Composition of Some proteins
47
tertiary structure of protein
Includes regular and irregular secondary structure and the spatial arrangement of the all the side chains.
48
Triose phosphate isomerase (TPI)
A typical globular protein; space filling, polypeptide backbone, ribbon diagram
49
General principles of gobular proteins.
* They contain at least two layers of secondary structure; protein has a definite surface and core region. * Hydrophobic core: typically 2° structure and h-bonds minimize hydrophilicity of the polar back bone. * Hydrophilic surface: typically with irregular structure and polar backbone groups of loops can form h-bonds with water.
49
General principles of gobular proteins.
They contain at least two layers of secondary structure; protein has a definite surface and core region.
50
Domain
A polypeptide segment that has been folded into a single structural unit with a hydrophobic core.
51
Growth hormone
An all alpha protein.
52
ab-crystallin
All b-protein. Only beta strands, anti-parallel that alternate. Non polar residues. Are connected through turns or loops.
53
Flvodoxin
a/b protein. Very structurally stable. It has 3 distinct layers.
54
Hydrophobicity and location
The greater the residue's hydrophobicity is, the more likely it is found within the protein's interior
55
ion pair
A charged residue in the protein interior that is located near another residue of opposite charge interact electrostatically to form an ion pair
56
Molecular chaperones
Proteins that assist smaller proteins to denature and renature within the cell. Helps them correctly fold.
57
Molecular chaperones
Proteins that assist smaller proteins to denature and renature within the cell. Helps them correctly fold.
58
A protein folding funnel
The folding process is not smooth or linear. The first stage of protein folding is known as the hydrophobic collapse; where the nonpolar groups are forced out of contact with water. Once the hydrophobic core takes shape the hydrogen bonding starts to from the secondary structure. And it then leads to the tertiary structure.
59
Quaternary Structure def.
The Spatial arrangement of more than one polypeptide chain in a protein. All the individual chains are known as subunits. When the subunits are incontact with one another there is a hydrophobic interaction. Uses the prefixes: homo- hetero and shorthand notation.
60
Subunits and the nomenclature
Homodimer, homotrimer and homotetramer. The homo means the same. And the di, tri and so one mean the amount of dimers. If the chains are not identical the hetero is used.
61
chromatography
Uses a column packed with porous mixture (the stationary phase) and a buffers solution (the mobile phase) that percolates through the column. The proteins and other solutes will go through the column at different rates depending on how the interact with the stationary phase.
62
Ion-exchange chromatography
A mixture of proteins is applied to the top of a positively charged anion exchange column. Negatively charged proteins bind to the matrix, while the uncharged and cationic proteins flow through the column. this process is for separating proteins in a solution based on differences in net charge. The neg charged proteins will bind to the pos charged solid supports. And vice versa
63
Gel filtration Chromatography/ size exclusion
Separation is based on size. Larger proteins migrate out of the column quicklier.
64
SDS-Page
For the purification of the protein. It has BME that is added to reduce disulfide bonds. and SDS is added to denature proteins and add a neg charge

Biochemistry (11 decks)

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