S1. Protein Structure

Question 1

Structure of amino acids.

Answer 1

Each amino acid (except for proline) has the following :

• α-carbon atom:
• carboxyl group (-COOH)
• amine group (-NH₂)
• hydrogen atom (-H)
• distinctive side chain (“R-group”)

Question 2

How are amino acids classified/different from another?

Answer 2

Amino acids are classified according to the properties of their side chains. These can be physical or chemical properties.

Amino acids are made up of peptide links and amino acid residues. The only independent variable in each protein is the amino acid residues.

Chemical properties of R groups

• Hydrophobic / Hydrophilic
• Polar / Non-polar
• Acidic / Basic / Neutral

Physical properties of R groups

• Aliphatic
  
  • Long Carbon chains
  • Only C & H atoms
• Aromatic
  
  • Benzene ring

Question 3

How do amino acids bond together?

Answer 3

Peptide bonds are formed to link two amino acids together accompanied by the abstraction/elimination of a molecule of water

Type of reaction : (condensation reaction/dehydration synthesis)

Question 4

Describe the 4 unique features of peptide bonds

Answer 4

• rigid
• planar
• exhibit a trans conformation
• bonds on either side of the peptide bond are free to rotate

Question 5

Why are peptide bonds rigid and planar?

Answer 5

The C-N bond in the peptide bond exhibits double bond characteristics.

• Due to the delocalisation of the electrons from the C=O bond.
• Cause the C-N bond to be shorter than expected.
• Therefore, peptide bond is more rigid, and this contributes to the peptide bond being planar.
• a-C, C, O, N, H, a-C are all in the same plane.

Question 6

How might amino acids be classified in terms of polarity?

Answer 6

• Polar: uneven distribution of electrons
• Nonpolar: even distribution of electrons

Question 7

Describe the structure and formation of a disulphide bond

Answer 7

• The side chain of cysteine contains a sulfhydryl group (–SH)
• In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulphide bond (–S–S–)

Question 8

What is the significance of disulphide bonds?

Answer 8

• Important component in the active site of many enzymes
• Many extracellular proteins are stabilized by disulphide bonds e.g. Albumin

Question 9

How can one characterise basic and acidic amino acids respectively?

Answer 9

• Acidic amino acids: negatively charged at physiological pH
• Basic amino acids: positively charged at physiological pH

Question 10

What is the value of physiological pH?

Answer 10

pH = 7.35 - 7.45

Question 11

Identify the 2 amino acids with acidic side chains

Answer 11

• Aspartate
• Glutamate

Question 12

Outline the behaviour of amino acids with acidic side chains

Answer 12

• The aspartic and glutamic acid are proton donors
• At physiological pH, the side chains of these amino acids are fully ionized, containing a negatively charged carboxylate group (–COO-)

Question 13

Outline the behaviour of amino acids with basic side chains

Answer 13

• The side chains of the basic amino acids accept protons
• At physiological pH the side chains of strongly basic amino acids are fully ionized and positively charged
• At physiological pH, the side chains of weakly basic amino acids the free amino acid is largely uncharged

Question 14

Identify the 3 amino acids with basic side chains

Answer 14

• Arginine (strongly basic)
• Lysine (strongly basic)
• Histidine (weakly basic)

Question 15

What is the Henderson-Hasselbalch equation?

Answer 15

Question 16

What is the significance of the Henderson-Hasselbalch equation?

Answer 16

The Henderson-Hasselbalch equation expresses the quantitative relationship between the pH of a solution and the [weak acid] and the [conjugate base]

Question 17

What encodes for the amino acid sequence of a protein?

Answer 17

The nucleotide sequence of a gene determines the amino acid sequence of a protein

Question 18

What is determined by the amino acid sequence of a protein?

Answer 18

• The way the polypeptide chain folds
• The physical characteristics of the protein

Question 19

Proteins are polypeptides.

What are polypeptides?

Answer 19

Polypeptides are macromolecules composed of amino acids

• Amino acids join covalently through peptide bonds to form the sequence of the protein

Question 20

Identify two contrasting factors which influences the way in which a protein folds?

Answer 20

• Chemical properties of the amino acids
• Physical properties of the amino acids

Question 21

How can amino acids be classified based on their chemical properties?

Answer 21

• Hydrophobic / Hydrophilic
• Polar / Non-polar
• Acidic / Basic / Neutral

Question 22

How can amino acids be classified based on their physical properties?

Answer 22

Aliphatic / Aromatic

Question 23

What are amino acid residues?

Answer 23

Amino acid residues are what remains of an amino acid after it has been joined by a peptide bond to form a protein

Question 24

How do pK_a values vary across acidic and basic amino acids?

Answer 24

- Basic amino acids:

I. Positively charged R groups

II. Higher pK_a values (6.0 - 12.5)

- Acidic amino acids:

I. Negatively charged R groups

II. Lower pK_a values (2.8 - 4.3)

Question 25

Illustrate the relationship between pK values and pH in terms of amino acids

Answer 25

- pH of the solution \< pK value of amino acid = **R group is protonated** - pH of the solution \> pK value of amino acid = **R group is deprotonated**

Question 26

What is meant by the isoelectric point of proteins?

Answer 26

**Isoelectric point (pI) of proteins:** the pI of a protein is the pH at which there is no overall net charge

Question 27

How do pI values vary across acidic and basic proteins?

Answer 27

- **Basic proteins** have a pI \> 7 and contain many positively charged (basic) amino acids - **Acidic proteins** have a pI \< 7 and contain many negatively charged (acidic) amino acids

Question 28

Illustrate the relationship between pI values and pH in terms of proteins

Answer 28

- If the pH \< pI then the protein is **protonated** - If the pH \> pI then the protein is **deprotonated**

Question 29

What are conjugated proteins?

Answer 29

Conjugated proteins are proteins which have other chemical components covalently linked in addition to amino acids *e.g. haemoglobin*

Question 30

Identify 5 biochemical roles of proteins

Answer 30

- **Catalysts** *e.g. enzymes* - **Transporters** *e.g. haemoglobin carries O₂* - **Structural support** *e.g. collagens in skin and bone* - **Immune protection** *e.g. immunoglobulins* - **Receptors** *e.g. for hormones, neurotransmitters, etc*

Question 31

Identify the 4 different components to protein structure

Answer 31

Question 32

Describe the primary structure of the protein

Answer 32

**Primary structure** is the linear amino acid sequence of the polypetide chain

Question 33

Describe the secondary structure of the protein

Answer 33

**Secondary structure** is the local spatial arrangement of polypeptide backbone consisting of alpha helixes and beta pleated sheets

Question 34

Which type of bond stabilises the secondary structure of a protein?

Answer 34

H₂ bonds

Question 35

Describe the tertiary structure of the protein

Answer 35

**Tertiary structure** is the overall 3D configuration of the protein

Question 36

Describe the quaternary structure of the protein

Answer 36

**Quaternary structure** is the association between different polypeptides to form a multi-subunit protein

Question 37

Identify the 4 interactions which stabilise the tertiary structure

Answer 37

- Disulphide bonds - Hydrophobic interactions - Hydrogen bonds - Ionic interactions

Question 38

Which bonds hold subunits together in the quaternary structure of the protein?

Answer 38

**Non-covalent interactions:** - Hydrogen bonds - Ionic bonds - Hydrophobic interactions

Question 39

How do subunits function in the quaternary structure of proteins?

Answer 39

- Subunits can function **independently** - Subunits can function **cooperatively** *e.g. haemoglobin*

Question 40

Describe the role and structure of fibrous proteins and include an example

Answer 40

- **Role**: support, shape, protection - **Structure**: single type of repeating secondary structure, forms long strands or sheets - **Examples**: collagen & keratin

Question 41

Describe the role and structure of globular proteins and include an example

Answer 41

- **Role**: catalysis, regulation, transport - **Structure**: several types of secondary structure - **Examples**: myoglobin, haemoglobin, carbonic anhydrase

Question 42

Identify the 2 types of secondary structures found in globular proteins

Answer 42

- Motifs - Domains

Question 43

Describe the 2 types of secondary structures found in globular proteins

Answer 43

- **Motifs** which are folding patterns containing 1/more elements of secondary structure - **Domains** which are the parts of a polypeptide chain that fold into a distinctive shape

Question 44

How do membrane proteins fold?

Answer 44

**Membrane proteins** fold to express hydrophobic amino acids on the exterior cell surface and hydrophilic amino acids on the interior forming channels

Question 45

How do water soluble proteins fold?

Answer 45

In **water soluble proteins,** polypeptide chains fold so the hydrophobic side chains are buried and polar and the charged side chains are on the cell surface

Question 46

Describe the relative amount of amino acids in the following: - Peptides/oligopeptides - Polypeptides/proteins

Answer 46

- **Peptides/oligopeptides:** few amino acids in length - **Polypeptides/proteins:** many amino acids in length