1. Protein Structure

Question 1

What bond joins amino acids?

Answer 1

Covalent bond

Question 2

What determines the folding of proteins?

Answer 2

The chemical and physical properties of the amino acid determined by the amino acid sequence

Question 3

What is the general structure of an amino acid?

Answer 3

Central carbon atom bonded to:

• NH2
• COOH
• R group
• Hydrogen atom

Question 4

How many amino acids are naturally found in our body?

Answer 4

20

Question 5

What is the structure of an ionised amino acid?

Answer 5

Central carbon atom:

• NH3+
• COO-
• R group
• Hydrogen atom

Question 6

What is an acid?

Answer 6

Proton donor

Question 7

What is a base?

Answer 7

Proton acceptor

Question 8

How are amino acids classified and why?

Answer 8

Based on the chemical properties of their R group as the rest of the amino acid is always the same

Question 9

What chemical properties are used to classify an amino acid?

Answer 9

Polar/Non-polar
Hydrophilic/Hydrophobic
Acid/Basic/Neutral

Question 10

What are the physical properties used to classify an amino acid?

Answer 10

Aromatic/Aliphatic (carbon ring present or not)

Question 11

What determines the polarity of an amino acid?

Answer 11

The interaction of the amino acid R group with water

Question 12

What is amino acid residue?

Answer 12

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

Question 13

What does a pK value tell you?

Answer 13

How likely it is that the amino acid will be ionised

Question 14

What is physiological pH?

Answer 14

7.4

Question 15

If the pH of solution < pK value then the group will be…

Answer 15

protonated

Question 16

If the pH of solution > pK value then the group will be…

Answer 16

deprotonated

Question 17

Define the primary structure of a protein

Answer 17

The specific linear amino acid sequence of the polypeptide chain

Question 18

Define the secondary structure of a protein

Answer 18

The local spatial arrangement of the polypeptide backbone (forms alpha helix or beta pleated sheet)

Question 19

Define the tertiary structure of a protein

Answer 19

The overall 3D configuration of the protein

Question 20

Define the quarternary structure of a protein

Answer 20

The association between different polypeptide chains to form a multi-subunit protein

Question 21

How are peptide bonds formed?

Answer 21

Hydrolysis (abstraction of a water molecule)

Question 22

What are 4 characteristics of peptide bonds?

Answer 22

• planar
• rigid (cant rotate)
• exist as trans in nature
• bonds on either side of peptide bond can rotate

Question 23

Why are peptide bonds rigid?

Answer 23

C-N has partial double bond characteristics as C=0 bond causes delocalisation of electrons in C-N causing the bond to be slightly shorter

Question 24

What is a Psi bond?

Answer 24

C-C

Question 25

What is a Phi bond?

Answer 25

C-N

Question 26

What is the isoelectric point (pI) of a protein?

Answer 26

The pH at which there is no overall charge

Question 27

What type of proteins are present when pI > 7?

Answer 27

Basic proteins

Question 28

What type of proteins are present when pI < 7?

Answer 28

Acidic proteins

Question 29

If pH > pI the protein is...

Answer 29

deprotonated

Question 30

If pH < pI the protein is...

Answer 30

protonated

Question 31

What determines the confirmation of the polypeptide backbone?

Answer 31

The bond angle of the C-C & C-N adjacent to the peptide bond

Question 32

State 4 properties of an alpha helix structure

Answer 32

- right handed helix structure - 3.6 amino acids per turn - trans orientated - hydrogen bonds between N-H & C=O (4 amino acids apart)

Question 33

What properties make it more likely for an alpha helix to form?

Answer 33

- small hydrophobic residue - possible bond angle rotations - R group (supports specific confirmations)

Question 34

State 4 properties of beta pleated strands

Answer 34

- fully extended confirmation (larger gap between amino acid residues) - trans - hyrogen bonding between each strand - 3 types of beta pleated strands

Question 35

What are the 3 types of beta pleated strands?

Answer 35

- Anti-parallel - Parallel - Mixed

Question 36

What are anti-parallel beta pleated sheets?

Answer 36

Adjacent beta strands run parallel in opposite directions allowing hydrogen bonds to form between each layer

Question 37

What are parallel beta pleated sheets?

Answer 37

Adjacent beta strands run parallel in the same direction allowing hydrogen bonds to form between layers (weaker H bonds as theyre at an angle)

Question 38

What are mixed beta pleated sheets?

Answer 38

Adjacent strands contain a mix of anti-parallel and parallel strands

Question 39

What is the role of fibrous proteins?

Answer 39

Support Shape Protection

Question 40

What is the structure of fibrous proteins?

Answer 40

long strans or sheets made from a single type of repeating secondary structure

Question 41

What is the role of globular proteins?

Answer 41

Catalysis (forms enzymes) | Regulation (forms transporter molecules)

Question 42

What is the structure of globular proteins?

Answer 42

Compact shape made of several types of secondary structure

Question 43

What is the structure of collagen?

Answer 43

Fibrous protein Alpha helix Triple helical arrangement Hydrogen bonding between chains

Question 44

How does the interaction of R groups with water affect the folding of water soluble proteins?

Answer 44

Polypeptides fold so hydrophobic chains are buried whilst hydrophilic chains are on the surface of the molecule as they like water interaction

Question 45

How does the polarity of proteins affect folding of the polypeptide?

Answer 45

Hydrohphilic chains buried and hydrophobic chains on cell surface membrane as hydrophobic chains want to interact with the membrane as theyre uncharged