Protein Structure and Function

Question 1

What makes cytosolic proteins and what makes secreted proteins and membrane proteins?

Answer 1

Ribosomes make cytosolic proteins. RER makes secreted and membrane proteins.

Question 2

Examples of structural proteins

Answer 2

Actin, microtubules, intermediate filaments

Question 3

Example of secreted protein

Answer 3

Hormones e.g. insulin

Question 4

Examples of molecular motors

Answer 4

DNA helicase, actin, myosin

Question 5

Example of secreted structural proteins

Answer 5

Collagen

Question 6

Example of intracellular protein, giving its function

Answer 6

Cytosolic signalling molecule- transfers signals from plasma membrane to the nucleus

Question 7

How to make all the different proteins from relatively limited number of genes?

Answer 7

SNPs, Post-translational modifications

Question 8

What are the two functional groups of amino acid?

Answer 8

Amino group, carboxylic acid group

Question 9

Why is the polypeptide backbone flexible?

Answer 9

So that it can bend and fold into many shapes for the secondary and tertiary structures.

Question 10

What determines folding of a protein?

Answer 10

Polarity (hydrophobic/hydrophilic) of side chains of amino acids

Question 11

What kind of bond do polar side chains form with water molecules

Answer 11

Hydrogen bonds

Question 12

What is the direction of an amino acid sequence?

Answer 12

Amino terminus to carboxyl terminus

Question 13

What directions can beta-pleated sheets go in?

Answer 13

Anti-parallel and parallel

Question 14

What two types of alpha helix are there?

Answer 14

Left-handed and right-handed

Question 15

Alpha helix

Answer 15

Polypeptide backbone folded into spiral. Shape forms due to hydrogen bonds between carbonyl groups and amine groups along chain. Side chains stick out at sides.

Question 16

Where are alpha helices abundant? How are they suited to this?

Answer 16

Abundant in membrane proteins. Hydrophobic side chains shield the hydrophilic backbone/alpha helix from lipid environment. Hydrophobic side chains interact with hydrophobic phospholipid tails. Hydrophilic parts of backbone form hydrogen bonds.

Question 17

Beta pleated sheet

Answer 17

Flat sheet made of laterally packed strands. Shape forms due to hydrogen bonds between carbonyl and amine groups of adjacent chains. Side chains above and below sheet. Strands antiparallel.

Question 18

Turn

Answer 18

Sharp bend redirecting polypeptide backbone

Question 19

Loop

Answer 19

A longer turn of the polypeptide backbone. Have hydrophilic residues and are found on surface of proteins

Question 20

Random coils

Answer 20

Polypeptide chains with random configuration

Question 21

Name 3 other secondary structures, other than beta or alpha.

Answer 21

Loops, turns, random coils

Question 22

Side chain interactions

Answer 22

VdW, Electrostatic attractions, hydrogen bonds (non covalent bonds). Spontaneous.

Question 23

Myoglobin secondary structure

Answer 23

Mainly alpha helices

Question 24

Tumour necrosis factor- secondary structure and what is it?

Answer 24

Mainly beta pleated sheet and it is an inflammatory cytokine

Question 25

What are barrels?

Answer 25

A tertiary structure formed by beta sheets that allow ions to pass through them

Question 26

Coiled coils, giving examples

Answer 26

Made of 2 or 3 alpha helices wound around each other. Hydrophobic amino acids line up where helices meet. Coiled coils give structural strength. Keratin and collagen

Question 27

Proteolytic cleavage

Answer 27

The process of breaking the peptide bonds between amino acids in proteins

Question 28

Post translational modifications. Name two examples.

Answer 28

A covalent processing event resulting from a proteolytic cleavage or additon of modifying group. Modulate the function of eukaryote proteins by altering activity state, localization, turnover, interactions with other proteins. Phosphorylation and Glycosylation.

Question 29

Phosphorylation

Answer 29

Addition of phosphate to amino acids

Question 30

Glycosylation

Answer 30

Addition of carbohydrates to specific sites on protein

Question 31

Disulphide bonds

Answer 31

A PTM. Stabilises tertiary structure. Formed between cysteines next to each other in folded structure. Do not alter shape. Generally found in excreted proteins, not cytosolic, because it’s a strong bond so gives secreted proteins strength for extracellular environment

Question 32

Reversible denaturation

Answer 32

Add solvent (acids or bases etc.) to disrupt non-covalent interactions. Protein loses secondary and tertiary structure and unfolds. If solvent is removed, protein refolds/renatures.

Question 33

Irreversible denaturation

Answer 33

Heat

Question 34

Why is protein folding possible naturally?

Answer 34

Because proteins always fold to lowest free energy. The process of folding is energetically favourable as it releases energy and increases entropy.

Question 35

Molecular chaperones. Name the two classes.

Answer 35

Proteins that bind to the partially folded polypeptide chains and assist them in folding. Two classes are chaperonins and heat shock proteins. Chaperones do not change 3D structure but speed up the process of folding and prevent aggregation and formation of non-productive intermediates.

Question 36

Aggregation

Answer 36

Different proteins all collecting up in one big group

Question 37

Why are molecular chaperones needed?

Answer 37

Because not all proteins fold simultaneously

Question 38

What is the charge of proteins dependent on?

Answer 38

Amino acid side chains

Question 39

Protein domains

Answer 39

Any segment of a polypeptide chain that can fold independently into a compact, stable structure. It is the modular unit from which larger proteins are made. Some proteins can form more than one domain. Each domain has different functions.

Question 40

Signal sequence

Answer 40

Part of the amino acid sequence that provides info as to where a protein should go after translation. Proteins without signal sequence remain in cytosol.

Question 41

Examples of diseases due to mutated/modified/misfolded

Answer 41

Cystic Fibrosis, Creutzfeldt-Jakob disease, Huntington’s, Alzheimer’s

Question 42

Cystic fibrosis

Answer 42

Inherited disease of secretory glands. DNA mutation (3 base pairs deleted) alters shape of a transmembrane protein which is involved in chloride transport. Impaired chloride transport leads to abnormal mucus which can cause recurrent bacterial infections and make it hard to breathe due to pulmonary obstruction.

Question 43

Creutzfeldt-Jakob disease

Answer 43

Misfolded prion proteins promote refolding of other prions into a disease conformation. The misfolded proteins form tightly packed beta-sheets. These build up in brain, forming amyloid plaques that cause death of nerves in death.

Question 44

Name one process in the cell to get rid of misfolding

Answer 44

Chaperones