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Proteins > Primary, Secondary, Tertiary & Quaternary Structure > Flashcards

Primary, Secondary, Tertiary & Quaternary Structure Flashcards

1
Q

What does the primary structure of a protein describe?

A

The amino acid sequence in a polypeptide

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2
Q

What does the secondary structure of a protein describe?

A

The local spatial arrangements of amino acids in the peptide chain

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3
Q

What does the tertiary structure of a protein describe?

A

The organisation of the primary and secondary structures into the 3D protein shape

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4
Q

What does the quaternary structure of a protein describe?

A

The arrangement of different subunits in a protein

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5
Q

What determines the primary structure of a protein?

A

The gene that codes for the protein

  1. the gene is transcribed to produce mRNA
  2. the mRNA is translated on the ribosome
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6
Q

What is so significant about the amino acid sequence of a protein?

A

This ultimately determines the structure and function of the folded protein

The unique properties of a protein is determined by the order of AAs and the R-groups they contain

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7
Q

What forms a polypeptide chain?

A

many amino acids joined by peptide bonds

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8
Q

How many amino acid residues are most natural proteins made up from?

A

50 - 2,000 amino acid residues

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9
Q

What is the backbone of an amino acid chain?

A

The backbone runs along the centre of the chain

It is alpha carbon atoms, each connected to the next by a peptide bond

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10
Q

What is meant by residues in an amino acid chain?

A

Amino acids within a polypeptide chain are residues

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11
Q

What is meant by ‘side chains’ within a polypeptide chain?

A

The different R-groups of amino acids are the side chains

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12
Q

What are the N-terminus and C-terminus within an amino acid chain?

A

The free amino group at one end is the N-terminus

The free carboxyl group at the other end is the C-terminus

This gives a polypeptide chain direction

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13
Q

What type of bond is a peptide bond?

How is it formed?

A

It is an amide bond

A condensation reaction occurs on the ribosome, and a water molecule is released

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14
Q

Why does the peptide bond not behave like a normal single covalent bond?

A

It resonates between 2 different structures

This means the C-N bond shows some double bond characteristics

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15
Q

What is significant about the peptide bond resonating between 2 forms?

A

This makes the peptide bond quite rigid

There is very limited rotation around the peptide bond

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16
Q

How are both forms of the secondary structure stabilised?

A

They are stabilised by hydrogen bonds arising between the O in the peptide bond, and the H atom attached to the N in another peptide bond

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17
Q

What forms the helix of an alpha-helix?

A

The helix is formed by the backbone of the chain

The sidechains extend outside of the helix

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18
Q

What type of helix is the alpha helix?

How many amino acid residues are there per turn?

A

The alpha helix is a right-handed helix

It has 3.6 residues per turn

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19
Q

What type of hydrogen bonds are present in the alpha helix?

A

intrachain hydrogen bonds

these are bonds between different parts of the same chain

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20
Q

Between which groups do the intrachain hydrogen bonds form in the alpha helix?

A

Hydrogen bonds between the N-H and the C=O groups of the main chain stabilise the helix

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21
Q

What gives the alpha helix some elasticity?

A

The fact that all the hydrogen bonds lie parallel to the alpha helix

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22
Q

How many strands make up the beta pleated sheet?

A

Polypeptide chains run alongside each other

There may be several strands making up a beta sheet

They may be different chains or different parts of the same chain

23
Q

Where are the side chains found on a beta pleated sheet?

A

The side chains lie above or below the plane of the sheet

24
Q

What types of hydrogen bonds stabilise the beta pleated sheet?

A

Hydrogen bonds between adjacent starnds

These may be intrachain or interchain

25
Q

What is the difference between intrachain and interchain hydrogen bonds?

A

Intrachain bonds are between 2 parts of the same chain

Interchain bonds are between different amino acid chains

26
Q

What gives the strands of a beta pleated sheet a pleated appearance?

How does this affect the properties of this secondary structure?

A

The tetrahedral angles separating the bonds on the carbon

This means the bonds are quite rigid and the structure has little elasticity

27
Q

How do the strands in a beta pleated sheet run?

A

The strands may run parallel to one another, or may be antiparallel

Loops and turns between the strands allow for a change in direction of the chain

28
Q

How is the arrangement of the tertiary structure described?

A

The structure is compact but there is some flexibility

29
Q

What amino acids tend to make up the interior of soluble proteins?

A

Hydrophobic amino acids

e.g. Leu, Val, Met, Phe

30
Q

What amino acids tend to make up the exterior of soluble proteins?

A

Hydrophilic amino acids

e.g. Arg, His, Lys, Asp, Gly

31
Q

Why is it significant that hydrophilic amino acids are on the exterior of the protein molecule?

A

Most proteins exist in a hydrophilic environment

32
Q

Why is the tertiary structure important?

A

It is important for the positioning of binding sites and active sites

The residues which make these up are not located very close together

33
Q

When does a protein have a quaternary structure?

A

A protein only has a quaternary structure if it is composed of several individual polypeptide subunits

34
Q

What stabilises the packing of helices, sheets and different subunits in proteins?

A

Side chain interactions

These may be covalent, but more often are non-covalent

35
Q

What is a disulphide bond?

A

A covalent bond between two cysteine amino acid residues

This is because cysteine contains the -SH thiol group

36
Q

What happens when 2 cysteine residues are brought in close proximity?

A

When they are brought in close proximity within a folded protein, the thiol groups react to form a disulphide bond

37
Q

What is the role of disulphide bonds in a quaternary structure?

What are some examples?

A

The disulphide bonds attach 2 different polypeptide chains to one another

e.g. insulin and antibodies

38
Q

What causes electrostatic interactions?

A

Attractions between charged amino acid side chains

39
Q

What is meant by an ion pair and a salt bridge?

A

the tertiary and quaternary structure are stabilised by electrostatic interactions between oppositely charged side chains

This is an ion pair and the interaction is a salt bridge

40
Q

What would happen if two similar charges were brought close together during the folding process?

A

They would repel each other

This would destabilise the structure

41
Q

In which molecules do van der waals interactions occur?

A

Van der Waals interactions occur in electrically neutral molecules

42
Q

What is involved in formation of van der waals interactions?

What makes them stronger?

A

They rely on the formation of dipoles (permanent or induced) of varying strength

The stronger the dipole, the stronger the interaction

43
Q

What creates a polar molecule?

A

When atoms of different elements are joined by a covalent bond, the two atoms attract the shared pair of electrons to different degrees

44
Q

What creates a dipole?

A

Covalent bonds with unequal electron sharing

A positive charge is concentrated towards one end and negative charge towards the other end

45
Q

What is a hydrogen bond?

A

An interaction between a hydrogen atom of a donor group and non-bonding electrons on an acceptor group

46
Q

What are examples of donor and acceptor groups?

A

Donor: -OH, =NH

Acceptor: O=C-

47
Q

How many amino acids can form hydrogen bonds?

A

Most of the polar residues

This is 12 out of the 20 amino acids

48
Q

What creates a temporary dipole?

A

Electrons may become temporarily unevenly distributed across a bond

This creates regions of slightly negative and slightly positive charges

49
Q

What causes a temporary dipole to form?

Is it constant?

A

It may occur by chance or be induced by the proximity of a charged atom

The dipole is constantly changing and will disappear and reform

50
Q

What creates an induced dipole from a temporary dipole?

A

When it becomes close to another molecule, the slightly negative end of the molecule will repel electrons in the neighbouring molecule

51
Q

What is the most important effect in stabilising proteins?

A

The hydrophobic effect

52
Q

What is meant by the hydrophobic effect?

A

Polar amino acids are found on the surface of the protein or are hydrogen-bonded in the core

Non-polar amino acids are buried in the core of the protein

53
Q

Why is it energetically most advantageous if non-polar molecules are found on the inside of proteins?

A

The presence of hydrophobic molecules interferes with hydrogen bonds between water molecules

Being in the core means they will not prevent H bonding any more than is necessary

Proteins (5 decks)

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