lecture 4 biochemistry (week 1)

Question 1

what is a proto-oncogene?

Answer 1

a proto-oncogene is a normal cellular gene that regulates cell growth and differentiation.

its primary function is to promote cell proliferation, survival, and division, allowing cells to grow and develop properly

when mutated they can cause normal cells to become cancerous

Question 2

what is c-Src?

Answer 2

it is the first proto-oncogene and a tyrosine kinase

Question 3

what is a tyrosine kinase?

Answer 3

a tyrosine kinase is a type of enzyme that catalyzes the transfer of a phosphate group from ATP (adenosine triphosphate) to a tyrosine residue in a protein’s side chain

Question 4

what are tyrosine kinases important in?

Answer 4

the processes of cell signalling, division, and metabolism

Question 5

describe the insulin receptor

Answer 5

the insulin receptor is an a2b2 polypeptide, held together by disulphide bonds

Question 6

what part of the insulin receptor does insulin bind to?

Answer 6

specifically binds to the a2 subunits

Question 7

what does the binding of insulin to the receptor cause?

Answer 7

a signal being transmitted to the b2 subunits which activates an intrinsic tyrosine kinase within the cytosolic domain of the b subunit - the signal has crossed the membrane

Question 8

describe insulin signalling in relation to the tyrosine kinase

Answer 8

the tyrosine kinase of the receptor phosphorylates specific Tyr residues within the receptor - autophosphorylation

these p-Tyr residues recruit signalling molecules to the receptor which are then phosphorylated

forms a signalling complex

Question 9

what is dimerization?

Answer 9

dimerization is the process of joining two identical or similar molecular entities by bond

Question 10

describe receptor activation after dimerization occurs

Answer 10

dimerization causes conformational changes bringing the tyrosine domains in close proximity - allows phosphorylation

Question 11

describe the structure of the EGF receptor

Answer 11

in its unbound state the receptor contains two identical but separated monomeric units - both contain a binding site

when EGF binds dimerization occurs

Question 12

what does ligand binding do in the context of this receptor?

Answer 12

ligand binding signal is transmitted across the membrane and the conformational change that results activates the intrinsic tyrosine kinase activity of the receptor.

consequence of ligand binding is the receptor gets auto phosphorylated

Question 13

describe trans auto phosphorylation

Answer 13

activation of the tyrosine kinase domain of the receptor then promotes phosphorylation of specific tyrosine residues within the receptor

the dimeric receptor phosphorylates trans
Chain A phosphorylates tyrosine in chain B and vice-versa

Question 14

what do photo-tyrosines do?

Answer 14

act as docking sites for signalling molecules

act as a magnet for the arrival of key signalling molecules

SH2 domains - an example of a protein domain found in many other types of protein - bind phospho-tyrosine residues

Question 15

describe the activation of tyrosine kinase receptors in relation to the SH2 domain

Answer 15

auto-phosphorylation of specific tyrosine residues function to recruit SH2 domain-containing proteins to the receptor

these are then activated –> signal propagated

different receptors recruit different SH2 domain containing proteins

Question 16

describe the characteristics of binding of the SH2 domains

Answer 16

all SH2 domains bind phospho-tyrosine

all SH2 domains have a pocket into which the P-Tyr residue fits

but not all bind all P-Tyr residues; there is a specificity dictated by the surrounding sequence in the target (receptor) polypeptide

two pronged plug concept

Question 17

summarize the signalling complex

Answer 17

specific ligand binds to specific receptor

dimerisation leads to activation of the receptor

tyrosine kinase domain (movement of activation loop)

autophosphorylation of specific tyrosine residues

recruits SH2 domain-containing proteins to the receptor

different receptors recruit different SH2 domain-containing proteins

different SH2 domains recognise P-Tyr in different sequence contexts

Question 18

give examples of a subset of SH2 domain containing proteins recruited by EGF receptors

Answer 18

PLC-gamma (SH3-SH2-kinase)

Ras-GAP (SH2-SH3-SH2–GTPase)

Question 19

describe the ligand dependant assembly of signalling molecules

Answer 19

localised to the receptor and activated with precise spatial and temporal coordinates

different receptors assemble different protein complexes depending on which effectors are recruited which in turn is a function of which proteins are expressed in a given cell type.

hence receptor-x can exert two distinct functions in two different cell types because the downstream effectors are different

Question 20

describe the steps after an increase in calcium is detected

Answer 20

signal molecule binds to GPCR –> GPCR subunit activates phospholipase C –> PhC breaks down PiP2 into and DAG and IP3 –> PKC binds to DAG –> activates PKC –> IP3 opens channel –> Ca binds to PKC

Question 21

what are RTKs

Answer 21

receptor tyrosine kinases (RTKs) are a subclass of tyrosine kinases

play a crucial role in mediating cell-to-cell communication, cell growth, motility, differentiation, and metabolism.

Question 22

describe the activation of PLCy by RTKs

Answer 22

PLC-γ recruited to receptor via specific SH2 domain

this brings PLC-γ into close proximity to the tyrosine kinase domain of the receptor.

PLC-γ is tyrosine phosphorylated and activated.

PLC-γ is now both active and near its substrate.

Question 23

what is a G protein?

Answer 23

also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells

Question 24

describe the MAPK cascade

Answer 24

Ras is a G-protein

Ras-GTP activates a signalling pathway

balance of Ras-GTP and Ras-GDP controlled by relative activity of Ras-GAP and SOS proteins

recruiting and activating these to receptors via SH2 domains is a key control step

Question 25

describe the pathway of MAP kinases

Question 26

what did peyton rous do?

Answer 26

discover a chicken sarcoma virus

Question 27

describe peyton rous’ experiment

Answer 27

remove sarcoma from a chicken’s breast muscle –> break into small tissue and grind up sarcoma with sand –> collect filtrate that has passed through fine pore filter –> inject filtrate into young chicken –> observe sarcoma in injected chicken

Question 28

can viruses cause cancer?

Answer 28

yes