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MCBG > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

what are proteins used for in biochemical processes?

A 
Catalysts e.g.enzymes
Transporters
Structural support 
Machines
Immune protection 
Ion channels
Receptors
Ligands in cell signalling
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2
Q

What are proteins made up of?

A

Amino acids

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3
Q

What bonds form in proteins?

A

Peptide

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4
Q

What determines the amino acid sequences of a protein?

A

The nucleotide sequence of a gene

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5
Q

What does the folding of a protein depend on?

A

3D shape depends on the chemical and physical properties of the amino acid

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6
Q

What is an amino acid made up of?

A

An amino group -NH2
A carboxyl group- COOH
A hydrogen atom
An R group

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7
Q

What is a zwitterion?

A

Ionised form of an amino acid

E.g. NH3+ and COO-

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8
Q

How are amino acids classified?

A 
According to the chemical properties of the r group:
Hydrophobic or hydrophilic
Polar or non-polar
Acidic, basic or neutral
Aliphatic or aromatic
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9
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 e.g. HNCHCH3CO

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10
Q

If the pK value is lower is the side chain more likely to be acidic or basic?

A

Acidic

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11
Q

If pK value is higher is the side chain more likely to be acidic or basic?

A

Basic

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12
Q

If the pH of the solution is lower than the pK them what will happen to the group?

A

It will be protonated

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13
Q

If the pH of the solution is greater than the pK value then what will happen to the group?

A

It will be deprotonated

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14
Q

What is primary structure?

A

The linear amino acid sequence of the polypeptide chain

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15
Q

What is secondary structure?

A

Local spatial arrange of polypeptide backbone e.g. Alpha helix

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16
Q

What is tertiary structure?

A

The overall 3D configuration of the protein

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17
Q

What is the quaternary structure?

A

Association between different polypeptides to form multi-subunit proteins

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18
Q

How are peptide bonds formed?

A

Linking of two amino acids by the abstraction of a water molecule

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19
Q

How do peptide bonds lie?

A

Planar

All lie in the same plane

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20
Q

Why are peptide bonds so rigid?

A

Has a partial double bond characteristic

Unable to rotate

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21
Q

Are peptide bonds cis or trans?

A

Trans

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22
Q

Which bonds in a peptide bond are free to rotate?

A

Bond on either side of the bond

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23
Q

What does the amino acid sequence of a protein determine?

A

The way in which the polypeptide chain folds and the physical characteristics of the protein

24
Q

What is the isoelectric point of a protein?

A

The pH at which there is no overall net charge

25
Q

What would the isoelectric point of basic proteins be?

A

Greater than 7

26
Q

What would the isoelectric points of acidic proteins be?

A

Less than 7

27
Q

If the pH is less than the isoelectric point of a protein is the protein protonated or deprotonated?

A

Protonated

28
Q

If the pH is more than the isoelectric point of a protein is the protein protonated or deprotonated?

A

Deprotonated

29
Q

What does the sequence determine for a protein?

30
Q

What does the structure determine for a protein?

31
Q

What bonds are present in the primary structure of a protein?

A

Peptide bonds

32
Q

What bonds are present in the secondary structure of a protein?

A

Hydrogen bonds between NH and CO

33
Q

How does an alpha helix form?

A

The CO group of one residue hydrogen binds to a NH of a residue 4 amino acids away

34
Q

What do Ala and Leu have in common?

A

Small and hydrophobic

Strong helix formers

35
Q

What does Pro do?

A

Helix breaker as rotation around N-C bond is impossible

36
Q

Why does Gly do?

A

Helix breaker as tiny R group supports other conformations

37
Q

How does a beta sheet form?

A

R groups alternate between opposite sides of the chain and hydrogen bonds form

38
Q

What is an example of an alpha helix?

39
Q

What is an example of a beta sheet?

A

Fatty acid binding protein

40
Q

What is an example of tertiary structure?

41
Q

What is a fibrous protein?

A

Support, shapes and protects
Long strands or sheets
Single type of repeating secondary structure
E.g. Collagen

42
Q

What is a globular protein?

A

Catalysis, regulation
Compact shape
Several types of secondary structure
Carbonic anhydrase

43
Q

What is collagen?

A

Triple helix arrangement
Gly- X- Y
Hydrogen bonds stabilise interactions between chains

44
Q

What is a motif?

A

Folding patterns containing 1 or more elements of secondary structure

45
Q

What is a domain?

A

Part of a polypeptide chain that folds into a distinct shape. Often has a specific functional role

46
Q

How do polypeptide chains fold?

A

So that hydrophobic side chains are buried and polar charged chains are on the surface
Except membrane proteins which are the opposite

47
Q

What are 2 examples of quaternary structures?

A

Haemoglobin and ribosomes

48
Q

What forces are present in tertiary and quaternary structures?

A

Covalent, ionic, H bonds, van see walls, hydrophobic

49
Q

What are disulphide bonds?

A

Formed between sys residues between two sulphurs

50
Q

What are electrostatic interactions?

A

Formed between charged groups e.g. Glu- or arg+

Relatively weak

51
Q

What are hydrogen bonds?

A

Bonds formed between electronegative atoms and a hydrogen bound to another electronegative atom

52
Q

What is hydrophobic effect?

A

Interactions between hydrophobic side chains due to displacement of water

53
Q

What is a van dear waals force?

A

Dipole dipole interactions

Important when surfaces of two large molecules come together

54
Q

How can proteins be denatured?

A

Disruption of protein structure can be done by breaking of forces holding the proteins together e.g. Heat (increased vibration energy) and pH ( alters ionisation states and changes bonds)

55
Q

How do proteins fold?

A

Ordered
Each step Localised folding and with stable conformations maintained
Driven by the need to find the most stable conformation

56
Q

What can protein misfolding cause?

57
Q

What are amyloid fibres?

A

Misfolded, insoluble form of a normally soluble protein
Highly ordered
Lots of beta sheet
Inter chain assembly stabilised by hydrophobic interactions between aromatic amino acids

MCBG (19 decks)

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