PROTEIN STRUCTURE

Question 1

Main roles of proteins

Answer 1

1. Structural: Cytoskeleton, long filamentous proteins that gives the cell structure
2. Catalysts: Enzymes (anabolic and catabolic)
3. Carriers/storage: Hemoglobin/ferritin (a protein that contains iron and is the primary form of iron stored inside of cells)
4. Protective: Antibodies
5. Signalling: Receptors, intracellular signalling
6. Channels: Transport through membranes, acts as barriers
7. Transporters: Transport through membranes and barriers
8. Cell adhesion: Extracellular matrix, stable layer of cells

Question 2

Characteristics of proteins

Answer 2

• determined by a unique amino acid sequence
• 2000-2500 human proteins
• long polypeptides flexible, allows proteins to fold
• each folded polypeptide chain has a specific shape

Question 3

How is the function of a protein determined?

Answer 3

Determined by both “external” chemistry and by shape, amino acid composition of the protein
-different amino acids have different properties both chemical and structural

Question 4

Primary structure of protein

Answer 4

The linear sequence of amino acids within a protein is considered the primary structure of the protein

• proteins are built from a set of only twenty amino acids, each of which has a unique side chain.
• the side chains of amino acids have different chemistries. The largest group of amino acids have nonpolar side chains
• Alanine, serine, leucine, lysine, tyrosine, valine, cysteine

Question 5

What is the N and C terminus?

Answer 5

The N-terminus is the START of a protein or polypeptide referring to the free amine group (-NH2) located at the end of a polypeptide

The C-terminus is the END of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH)

Question 6

What is the R group on an amino acid?

Answer 6

The variant group

• gives the amino acid its particular structure and chemistry
• there are 20 different R groups which results in a variety of chemical properties which different amino acids have (hydrophilic/hydrophobic, polar/nonpolar, structural, chemistry)

Question 7

Typical structure of an amino acid

Answer 7

1. Amino group (NH3+)
2. Hydrogen
3. Carboxyl (C=O)
4. R group
5. Chiral carbon

Question 8

What are non-polar aliphatic (no charge) R groups?

Answer 8

Glycine, alanine, proline, valine, leucine, isoleucine and methionine

Question 9

What are aromatic (benzene ring) R groups?

Answer 9

Phenylalanine, tyrosine and tryptophan

Question 10

What are polar, uncharged R groups?

Answer 10

Serine, threonine, cysteine, asparagine and glutamine

Question 11

What are positively charged R groups?

Answer 11

Lysine, arginine and histidine

Question 12

What are negatively charged R groups?

Answer 12

Aspartate and glutamate

Question 13

How is protein formed from amino acids?

Answer 13

A string of amino acids folds up

• non-polar hydrophobic amino acid in the center of a folded protein
• polar amino acid on the outside, in contact with the water in the cytosol

Question 14

What is the peptide bond?

Answer 14

A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein chain

• the essential bond in protein
• molecule of water is lost from two linking amino acids, condensation reaction

Question 15

What is the general structure of a peptide?

Answer 15

Two or more amino acids joined through amide formation involving the carboxyl group of each amino acid and the amino group of the next

• Amino terminal end (NH3+)
• Carboxyl terminal end (COO-)

Question 16

Secondary structure of protein

Answer 16

The three dimensional form of local segments of proteins

• the two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well
• determined by interactions between the peptide bonds via hydrogen bonding

Question 17

What is the A-helix in the secondary structure of proteins?

Answer 17

Stabilised by hydrogen bonds between carbonyl oxygen and the amino group of every third residue in the helical turn with each helical turn consisting of 3.6 amino acid residues

• side chain of amino acids is projected outward from the outer helical surface
• at every turn of the helix, there are certain amino acids that can interact with each other and form H bonds
• R groups are. hydrophilic and point away from the alpha helix

Question 18

What are B sheets in the secondary structure of proteins?

Answer 18

Flat sheet surface with strands of protein

• stabilised by hydrogen bonds between amide links
• strands can be parallel or anti-parallel
• beta sheets can be stacked to form a 3D tertiary structure

Question 19

What does disorder in protein structure mean?

Answer 19

Areas of a protein can be disordered, they do not have an alpha helical or b pleated sheet structure

• can form a structure on something else
• contradicts lock and key model
• disordered regions of proteins often involved in protein interaction are rich in polar and charged residues so they are hydrophilic

Question 20

Tertiary structure of protein

Answer 20

General folding of the polypeptide into its final 3D shape

• determined by the primary structure (amino acid sequence) and R groups
• disulphide bond formed, which stabilises the tertiary structure
• collagen is tertiary structure, triple helix with a large number of prolines in a “Pro-Pro-Gly”, the staggering of the 3 chains helps hydrogen bonding between chains, further post translational modification enables covalent strand crosslinks, these include disulphide between cysteine and lysine cross linking, giving a strong and stable structure

Question 21

Quaternary structure of protein

Answer 21

The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement.

• each of the subunits has its own primary, secondary, and tertiary structure
• the subunits are held together by hydrogen bonds and van der Waals forces between non-polar side chains
• can be homo or hetero
• Haemoglobin is an example: 4 alpha helices and 4 subunits (2 alpha and 2 beta)

Question 22

How are proteins named?

Answer 22

Based on their 3D shape

1. Globular
   - majority of proteins
   - overall globular shape with a mix of secondary structures
2. Fibrous
   - extensive packing of secondary structures
   - dominated by one type of secondary structure
   - forms structural proteins (eg. collagen/keratin)
   - proteins can be made up of domains, discrete regions of 3D structure

Question 23

How do we go from a peptide chain to a fully folded protein?

Answer 23

Spontaneous folding driven to minimise energy

• hydrophobic effect
• hydrogen/polar bonding
• not all proteins can spontaneously fold
• as the protein folds, the amount of energy within that protein and the energy required decreases

Question 24

What are chaperones?

Answer 24

Helper proteins that aid in protein folding

• diverse group of proteins
• levels of chaperones increases when the cell is subjected to stress
• some binds to hydrophobic residues and prevent hydrophobic effect driven folding
• some act to protect the folding protein from unfolding
• uses ATP to provide energy to the folding process

Question 25

What are post translational modification?

Answer 25

Adaptations that happen to proteins after they have been translated, allowing for the modifications of the function of a protein

• addition of other functional groups (acetate, phosphate, lipids)
• addition of protein/peptides
• changing the chemical nature of amino acids (denaturation, elimination)
• structural changes (disulphide cleavage)

Question 26

Where does phosphorylation occur?

Answer 26

On serine, threonine and tyrosine residues

Question 27

How are disulphide bonds formed?

Answer 27

Occurs between cysteine residues

• covalent links
• stabilises a 3D structure
• requires a specific redox environment to form

Question 28

What is proteolytic cleavage?

Answer 28

Proteolytic cleavage is basically the process of breaking the peptide bonds between amino acids in proteins.

• this is carried out by enzymes called peptidases, proteases or proteolytic cleavage enzymes
• eg. processing of pre-proinsulin

Question 29

What is process of ubiquitination?

Answer 29

Small protein added to another, acts in signalling and degradation

Question 30

What is the process of deamination?

Answer 30

Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminase

• spontaneous chemical reaction in physiological conditions but can be reduced by removing reactive species from the cytosol
• results in structural changes and protein damage
• plays a role in aging, autoimmune disorders (celiac disease), neuro-degeneration (Alzheimers disease)