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Flashcards in Protein Structure Deck (57):
1

what are proteins used for in biochemical processes?

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

2

What are proteins made up of?

Amino acids

3

What bonds form in proteins?

Peptide

4

What determines the amino acid sequences of a protein?

The nucleotide sequence of a gene

5

What does the folding of a protein depend on?

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

6

What is an amino acid made up of?

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

7

What is a zwitterion?

Ionised form of an amino acid
E.g. NH3+ and COO-

8

How are amino acids classified?

According to the chemical properties of the r group:
Hydrophobic or hydrophilic
Polar or non-polar
Acidic, basic or neutral
Aliphatic or aromatic

9

What is an amino acid residue?

What remains of an amino acid after it has been joined by a peptide bond to form a protein e.g. HNCHCH3CO

10

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

Acidic

11

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

Basic

12

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

It will be protonated

13

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

It will be deprotonated

14

What is primary structure?

The linear amino acid sequence of the polypeptide chain

15

What is secondary structure?

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

16

What is tertiary structure?

The overall 3D configuration of the protein

17

What is the quaternary structure?

Association between different polypeptides to form multi-subunit proteins

18

How are peptide bonds formed?

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

19

How do peptide bonds lie?

Planar
All lie in the same plane

20

Why are peptide bonds so rigid?

Has a partial double bond characteristic
Unable to rotate

21

Are peptide bonds cis or trans?

Trans

22

Which bonds in a peptide bond are free to rotate?

Bond on either side of the bond

23

What does the amino acid sequence of a protein determine?

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

24

What is the isoelectric point of a protein?

The pH at which there is no overall net charge

25

What would the isoelectric point of basic proteins be?

Greater than 7

26

What would the isoelectric points of acidic proteins be?

Less than 7

27

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

Protonated

28

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

Deprotonated

29

What does the sequence determine for a protein?

Structure

30

What does the structure determine for a protein?

Function

31

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

Peptide bonds

32

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

Hydrogen bonds between NH and CO

33

How does an alpha helix form?

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

34

What do Ala and Leu have in common?

Small and hydrophobic
Strong helix formers

35

What does Pro do?

Helix breaker as rotation around N-C bond is impossible

36

Why does Gly do?

Helix breaker as tiny R group supports other conformations

37

How does a beta sheet form?

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

38

What is an example of an alpha helix?

Ferritin

39

What is an example of a beta sheet?

Fatty acid binding protein

40

What is an example of tertiary structure?

Myoglobin

41

What is a fibrous protein?

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

42

What is a globular protein?

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

43

What is collagen?

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

44

What is a motif?

Folding patterns containing 1 or more elements of secondary structure

45

What is a domain?

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

46

How do polypeptide chains fold?

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

47

What are 2 examples of quaternary structures?

Haemoglobin and ribosomes

48

What forces are present in tertiary and quaternary structures?

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

49

What are disulphide bonds?

Formed between sys residues between two sulphurs

50

What are electrostatic interactions?

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

51

What are hydrogen bonds?

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

52

What is hydrophobic effect?

Interactions between hydrophobic side chains due to displacement of water

53

What is a van dear waals force?

Dipole dipole interactions
Important when surfaces of two large molecules come together

54

How can proteins be denatured?

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

How do proteins fold?

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

56

What can protein misfolding cause?

Disease

57

What are amyloid fibres?

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