Protein Structure

Question 1

what are proteins used for in biochemical processes?

Answer 1

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

Question 2

What are proteins made up of?

Answer 2

Amino acids

Question 3

What bonds form in proteins?

Answer 3

Peptide

Question 4

What determines the amino acid sequences of a protein?

Answer 4

The nucleotide sequence of a gene

Question 5

What does the folding of a protein depend on?

Answer 5

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

Question 6

What is an amino acid made up of?

Answer 6

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

Question 7

What is a zwitterion?

Answer 7

Ionised form of an amino acid

E.g. NH3+ and COO-

Question 8

How are amino acids classified?

Answer 8

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

Question 9

What is an amino acid residue?

Answer 9

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

Question 10

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

Answer 10

Acidic

Question 11

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

Answer 11

Basic

Question 12

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

Answer 12

It will be protonated

Question 13

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

Answer 13

It will be deprotonated

Question 14

What is primary structure?

Answer 14

The linear amino acid sequence of the polypeptide chain

Question 15

What is secondary structure?

Answer 15

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

Question 16

What is tertiary structure?

Answer 16

The overall 3D configuration of the protein

Question 17

What is the quaternary structure?

Answer 17

Association between different polypeptides to form multi-subunit proteins

Question 18

How are peptide bonds formed?

Answer 18

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

Question 19

How do peptide bonds lie?

Answer 19

Planar

All lie in the same plane

Question 20

Why are peptide bonds so rigid?

Answer 20

Has a partial double bond characteristic

Unable to rotate

Question 21

Are peptide bonds cis or trans?

Answer 21

Trans

Question 22

Which bonds in a peptide bond are free to rotate?

Answer 22

Bond on either side of the bond

Question 23

What does the amino acid sequence of a protein determine?

Answer 23

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

Question 24

What is the isoelectric point of a protein?

Answer 24

The pH at which there is no overall net charge

Question 25

What would the isoelectric point of basic proteins be?

Answer 25

Greater than 7

Question 26

What would the isoelectric points of acidic proteins be?

Answer 26

Less than 7

Question 27

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

Answer 27

Protonated

Question 28

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

Answer 28

Deprotonated

Question 29

What does the sequence determine for a protein?

Answer 29

Structure

Question 30

What does the structure determine for a protein?

Answer 30

Function

Question 31

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

Answer 31

Peptide bonds

Question 32

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

Answer 32

Hydrogen bonds between NH and CO

Question 33

How does an alpha helix form?

Answer 33

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

Question 34

What do Ala and Leu have in common?

Answer 34

Small and hydrophobic | Strong helix formers

Question 35

What does Pro do?

Answer 35

Helix breaker as rotation around N-C bond is impossible

Question 36

Why does Gly do?

Answer 36

Helix breaker as tiny R group supports other conformations

Question 37

How does a beta sheet form?

Answer 37

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

Question 38

What is an example of an alpha helix?

Answer 38

Ferritin

Question 39

What is an example of a beta sheet?

Answer 39

Fatty acid binding protein

Question 40

What is an example of tertiary structure?

Answer 40

Myoglobin

Question 41

What is a fibrous protein?

Answer 41

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

Question 42

What is a globular protein?

Answer 42

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

Question 43

What is collagen?

Answer 43

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

Question 44

What is a motif?

Answer 44

Folding patterns containing 1 or more elements of secondary structure

Question 45

What is a domain?

Answer 45

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

Question 46

How do polypeptide chains fold?

Answer 46

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

Question 47

What are 2 examples of quaternary structures?

Answer 47

Haemoglobin and ribosomes

Question 48

What forces are present in tertiary and quaternary structures?

Answer 48

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

Question 49

What are disulphide bonds?

Answer 49

Formed between sys residues between two sulphurs

Question 50

What are electrostatic interactions?

Answer 50

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

Question 51

What are hydrogen bonds?

Answer 51

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

Question 52

What is hydrophobic effect?

Answer 52

Interactions between hydrophobic side chains due to displacement of water

Question 53

What is a van dear waals force?

Answer 53

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

Question 54

How can proteins be denatured?

Answer 54

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)

Question 55

How do proteins fold?

Answer 55

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

Question 56

What can protein misfolding cause?

Answer 56

Disease

Question 57

What are amyloid fibres?

Answer 57

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