Protein Structure Flashcards

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1
Q

What is the general structure of an amino acid?

A

A central carbon has an amino group, carboxyl group, a hydrogen atom and an R group covalently bonded to it

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2
Q

In what state are amino acids usually present as?

A

Zwitter Ions

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3
Q

What is an amino acid residue?

A

What remains of an amino acid after it has been joined by a peptide bond to form a protein

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4
Q

If an amino acid has a high PKA value what does that indicate?

A

It is a basic amino acid

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5
Q

What is pKa?

A

pKa tells you the strength of an acid, so how likely the groups are to lose or gain protons

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6
Q

If the pH is less than then pKa value what will happen to the side group?

A

The group is more likely to be protonated

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7
Q

What is the primary structure of a protein?

A

The amino acid sequence of the polypeptide chain

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8
Q

What is the secondary structure?

A

The way the chains fold into conformations like helices etc

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9
Q

What is the tertiary structure?

A

The overall 3D shape

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10
Q

What is the quaternary structure?

A

The association between different polypeptides to form a multi-subunit protein

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11
Q

In what type of reaction are peptide bonds formed?

A

A condensation reaction so a molecule of water is released

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12
Q

What does it mean by saying that peptide bonds are planar?

A

The atoms all lie in the same plane

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13
Q

Why can’t peptide bonds rotate?

A

Electrons from the C=O bond of the carboxyl group move between the central carbon and nitrogen from the amino group giving it double bond properties (resonance)

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14
Q

Why do peptide bonds also have trans conformations?

A

By having the central carbon on opposite sides of the peptide bonds, the R groups will be further apart so won’t repel

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15
Q

Why is the amino acid sequence important?

A

It determines the physical characteristic and the way in which the protein folds

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16
Q

What is the ISO electric point of a protein?

A

The pH at which there is no overall net charge

17
Q

What happens if the pH is less than pI?

A

The amino acids will be protonated

18
Q

What are conjugated proteins?

A

Proteins that are covantely linked to other chemical components as well as amino acids e.g. Glycoproteins

19
Q

What binds hold the alpha helix structure together

A

Hydrogen bonds between the amino group and the carboxyl group

20
Q

What 2 arrangements can be made from proteins with a beta sheet secondary structure?

A

Antiparallel and parallel sheets

21
Q

Why are parallel beta sheets weaker than antiparallel sheets?

A

As the beta strands are running in the same direction the hydrogen bonds are at an angle and so are weaker

22
Q

What is the domain of a globular protein?

A

Where part of a polypeptide chain folds into a distinct shape and often has a specific role

23
Q

What are the 2 different types of tertiary structure?

A

Fibrous and Globular

24
Q

How can amino acids be classified?

A

By whether they are:

  • hydrophilic/hydrophobic
  • polar/non-polar
  • basic/acidic/neutral
  • aliphatic/aromatic
25
Q

If an amino acid has a charge will it be hydrophobic or hydrophilic

A

Hydrophilic

26
Q

What does it mean if the pKa is equal to pH?

A

There will be equal amounts of protonated and deprotonated forms

27
Q

What is the Henderson-Hasselbach equation?

A

pH = pKa + log(base/acid)

28
Q

What bonds hold the tertiary structure together?

A

Ionic, H bonds, covalent, Van der Walls and hydrophobic and disulphide bonds

29
Q

Between which amino acid residues do disulphide binds form?

A

Cystine

30
Q

What properties do disulphide bonds give to proteins

A

The binds help keep the structure better so they can withstand hostile environments

31
Q

Between what groups do electrostatic interactions occur

A

Oppositely charged groups

32
Q

What is the hydrophobic effect?

A

Interactions between hydrophobic side chains result in the exclusion of water

33
Q

What determines how a protein folds?

A

Primary sequence

34
Q

How do proteins fold?

A

There is localised folding to form stable conformations

35
Q

What is amyloidosis

A

A condition when their are deposits of amyloid fibres (misfolded, insoluble protein)