Proteins

Question 1

What are the stages of protein transcription?

Answer 1

RNA polymerase binds to promoter (start sequence) and Helicase unwinds DNA
Free RNA nucleotides pair up to the complementary bases on the exposed DNA strand (Thymine is replaced by Uracil)
RNA polymerase joins the nucleotides with phosphodiester bonds until the terminator (stop sequence) forming a mRNA strand
The DNA rewinds and mRNA leaves through a nuclear pore

Question 2

What are the stages of protein translation and modification?

Answer 2

Ribosome moves along mRNA attaching tRNA molecules (3 bases/amino acids/anti-codons) (uracil is replaced by thymine)
The amino acids are linked into a peptide chain which is released into the cis-ER and packaged into a vesicle
The vesicle is sent out of the trans-ER to the Golgi where it is modified and sorted

Question 3

How do Antibiotics work?

Answer 3

Inhibiting prokaryotic ribosomes

Preventing the formation of a cell wall

Question 4

What is the general structure of an amino acid?

What is the structure of a zwitterion of an amino acid?

What is a peptide bond?

Answer 4

H2N - (H)C(R) - COOH

(H3N+) - (H)C(R) - COO-

a.a.1 - C(O) - N(H) - a.a.2

Question 5

What type of bonds are involved and what determines the primary structure of proteins?

Answer 5

Covalent peptide bonds forms the linear polymer of amino acids
Determined by the sequence of nucleotides in a gene

Question 6

What are the features of the primary structure of proteins?

Answer 6

Always:
Planar (all molecules lie in the same line)
Rigid (C-N is a partial double bond with no rotation)
Trans (R-groups can have steric clashes with cis-kinks)

Question 7

What type of bonds are involved and what determines the secondary structure of proteins?

Answer 7

H-bonds bonds form the local spatial arrangement of polypeptide chains
Determined by the sequence of amino acids

Question 8

What are the types of secondary structures of proteins possible?

Answer 8

Alpha-helices: Always right-handed with H-bonds between C=O and N-H 4 amino acids away
Beta-strands: Polypeptide chain with R-groups on alternate sides
Beta-sheets: H-bonds form between beta-strands (antiparallel, parallel, mixed)

Question 9

What type of bonds are involved and what determines the tertiary structure of proteins?

Answer 9

All types of bonds/attractions form the overall 3D shape of the polypeptide
Determined by the chemical and physical properties of amino acids

Question 10

What are the types of tertiary structures of proteins possible?

Answer 10

Fibrous:
Long strands/sheets of a single repeating secondary structure
Support, Shape, Protect
Globular:
Compact shape made of several different secondary structures
Catalysis, Regulation

Question 11

What type of bonds are involved and what determines the quarternary structure of proteins?

Answer 11

All types of bonds/attractions form the overall multi-subunit protein
Determined by the interactions of the polypeptide chains

Question 12

What are phi and psi bonds and what structure do they influence?

Answer 12

Influence secondary structure (able to rotate)
Phi bond: bond between (H2)N - C
Psi bond: bond between C - C(OOH)

Question 13

What are disulphide bonds and what structure do they influence?

Answer 13

Influence the tertiary structure (interactions of amino acids)
Bonds between 2 SH (cysteine) R-groups
The R-groups are oxidised to form S-S (cystine) bond
(Found on secreted proteins as the S-S bond is unstable in the cytoplasm, can also be destroyed by reducing agents)

Question 14

What is the hydrophobic effect and what structure does it influence?

Answer 14

Influences tertiary structure (inner hydrophobic amino acids)
Not a bond
Attraction between non-polar (hydrophobic) molecules when they are forced together by excluding H2O

Question 15

How are proteins folded?

Answer 15

The information on the folding of a protein is contained within the primary sequence of a protein
Localised folding with maintained stable conformations allow the protein to ‘find’ its structure

Question 16

How are proteins denatured?

Answer 16

Heat
pH
Organic solvents

Question 17

What is the isoelectric point?

Answer 17

pH at which the amino acid has no charge (forms the zwitterion)

Question 18

What happens to an amino acid when:
pKa < pH
pKa > pH

Answer 18

pKa < pH: deprotonated

pKa > pH: protonated

Question 19

What are isoenzymes?

What are co-enzymes?

Answer 19

Isoenzymes: different form of the same enzyme (same function) formed from different splicing of the same gene resulting in different kinetic properties

Coenzymes: non-protein molecules that bind to the enzyme to activate it

Question 20

Describe what product inhibition is

Answer 20

Accumulation of the product inhibits the forward reaction

Question 21

Describe what the T and R states of an enzyme are and explain the action of inhibitors and activators

Answer 21

T-state: low affinity for substrate
R-state: high affinity for substrate
Inhibitors: Increase the proportion of T-state enzymes
Activators: Increase the proportion of R-state enzymes

Question 22

Describe the action of Kinase and Phosphatase

Answer 22

Kinase: Transfers the phosphate group from ATP onto the hydroxy group of Serine, Threonine, Tyrosine

Phosphatase: Removes the phosphate group from the hydroxy group of Serine, Threonine, Tyrosine by hydrolysis

Question 23

Describe what phosphorylation (Kinase) does to proteins and how it can be controlled

Answer 23

Adds a negative charge (can form H-bonds)

Increase the amount ATP, Increase the rate of phosphorylation that can occur

Question 24

Explain how Chymotrypsinogen is activated in the pancreas

Answer 24

Enteropeptidase is released by the pancreas
Enteropeptidase cleaves trypsinogen —> trypsin
Trypsin cleaves chymotrypsinogen —> pi-chymotrypsin
Chymotrypsin cleaves pi-chymotrypsin —> alpha-chymotrypsin

Question 25

What is a zymogen?

Answer 25

Inactive form of an enzyme

Question 26

Explain how proteolytic cleavage is regulated

Answer 26

Short-term:
Substrate and Product concentrations
Enzyme conformation (allosteric, affinity)

Long-term:
Protein synthesis and degradation

Question 27

What is the body response to bleeding?

Answer 27

Primary haemostasis:
Vasoconstriction (reduced blood flow)
Platelet aggregation

Secondary haemostasis:
Coagulation (liquid blood —> gel clot)

Question 28

How do platelets aggregate?

Answer 28

Glycoproteins on the surface of platelets bind to Von Willebrand Factor (vWF) on collgen fibrils
vWF is released from granules in platelets trapping more platelets
vWF stabilises Factor VIII (antihaemophilic)

Question 29

Describe the intrinsic pathway to coagulation

Answer 29

Exposure to negatively charged surface (phospholipids, cholesterol) activates FXI —> FXIa
FIX —> FIXa (FXIa)
FX —> FXa (FIXa with FVIIIa)

Question 30

Describe the extrinsic pathway to coagulation

Answer 30

Vascular damage resulting in release of FIII from Intracellular region activating it to form FIIIa
FVII —> FVIIa (FIIIa)
FX —> FXa (FVIIa)

Question 31

Describe the common pathway to coagulation

Answer 31

Prothrombin —> Thrombin (FVa with FXa)
Fibrinogen —> Fibrin (Thrombin)
Formation of cross-linked fibrin with FXIIIa

Question 32

What is Prothrombin made up of and what are their functions?

Answer 32

Gla domain: targets polypeptide to sites for activation and acts as a magnet for other clotting factors
Kringle loops: keep the polypeptide in its inactive form
Serine protease: cointained within the C-terminal

Question 33

What are Gla-domains and how are they formed?

Answer 33

G-carboxyglutamate domains found in factors II (Prothrombin), VII, IX, X
Domains that have been post-translationally modified in the liver by the addition of COOH groups to glutamate residues (carboxylation)

Question 34

How do Gla domains ensure local response?

Answer 34

Gla binds with Ca2+ at the damaged site activating Thrombin only at the site of damage and attracting other clotting factors

Question 35

What is the structure of fibrinogen?

Answer 35

Formed of a pair of tripeptides (alpha, beta, gamma) joined at the N-terminus by Disulphide bonds
Beta and gamma C-terminus are globular domains which form a globular unit
Beta and alpha are negatively charged and prevent aggregation of fibrinogen

Question 36

How does a fibrin clot form?

Answer 36

Activation:
Thrombin activates fibrinogen forming fibrin by cleaving the alpha and beta N-termini (releasing negatively charged domains)
Polymerisation:
The globular units joins with the exposed beta and alpha termini to form a fibrin mesh
Formation of amide bonds:
Transglutaminase (activated by thrombin from protransglutaminase) forms amide link between Lysine and Glutamine residues on each monomer

Question 37

What is classic haemophilia?

What is Haemophilia B?

Answer 37

Haemophilia is the inability to form clots
Haemophilia A: Unactivated FVIII (antihaemophillic factor) limited proteolysis by Thrombin and FXa
Haemophilia B: Deficiencies in FIX and the intrinsic pathway

Question 38

How is the clotting process stopped?

Answer 38

Dilution of clotting factors (blood flow increases after vasodilation)
Inactivation of clotting factors by Protein C
Inhibitors of clotting factors

Question 39

What is the role of Protein C?

Answer 39

Protein C is activated by Thrombomodulin an Endothelial Protein C Recptor (EPCR)
The binding of Protein C and Thrombin to an EPCR activates Protein C which inactivates FVa and FVIIIa through hydrolysis

Question 40

What is an inhibitor involved in stopping the clotting cascade?

Answer 40

AT-3 (Anti-Thrombin 3)
Binds to Thrombin, FIXa, FXa, FXIa, FXIIa
Heparin (Anticoagulent) increases the affinity of AT-3 for Thrombin

Question 41

How is the clot broken down?

Answer 41

Fibrinolysis: proteolysis of fibrin —> fibrin fragments
Plasminogen is activated to form plasmin by t-PA and streptokinase
Plasmin breaks down fibrin clots