Lecture 16: Regulation of protein function and enzymes

Question 1

Enzymes are:

Answer 1

proteins folded into complex shapes that allow substrate molecules to fit into the active site

Question 2

Enzymes do not

Answer 2

change during reactions, nor do they change the other contents of the reaction. They simply facilitate the interaction of reactants and speed up the rate of the reaction.

Question 3

Enzymes are the most:

Answer 3

selective and powerful catalysts known

Question 4

hydrolases:

Answer 4

hydrolytic cleavage (including nucleases and proteases)

Question 5

Nucleases :

Answer 5

break down nucleic acids by hydrolysing bonds between nucleotides

Question 6

Proteases:

Answer 6

Break down proteins by hydrolysing bonds between amino acids

Question 7

Syntheses:

Answer 7

Synthesise molecules by condensing two small molecules

Question 8

Isomerases:

Answer 8

Rearrangement of bonds within a single molecule

Question 9

Polymerases:

Answer 9

Polymerisation reactions such as synthesis of RNA and DNA

Question 10

Kinases

Answer 10

Addition of phosphate to molecules (e.g. sugars, proteins)

Question 11

Phophatases:

Answer 11

Removal of phosphate group

Question 12

Oxide-Reductases:

Answer 12

One molecule is oxidised while another is reduced

Question 13

ATPases:

Answer 13

Hydrolyse or synthesise ATP

Question 14

Total number of enzyme in man is

Answer 14

~75,000

Question 15

Many enzyme require:

Answer 15

cofactors, such as metal ions, NAD(P)(H), ATP, Vitamins etc

Question 16

the function of over 60% of plant enzymes is

Answer 16

unknown

Question 17

The ___ regulates the catalytic activity of enzymes

Answer 17

cell

Question 18

regulation of enzyme protein abundance is by

Answer 18

transcription and translation

Question 19

Direct fine-tuned control of protein activity and kinetics is by

Answer 19

metabolites and regulators (which could affect many enzymes)

Question 20

Cell regulates enzymes for

Answer 20

specific post-translational modifications (specific covalent modifications affecting one single step)

Question 21

Feedback inhibition in a metabolic pathway: bacterial pathway for tryptophan synthesis

Answer 21

• Trp can inhibit the activity of the first enzyme in the pathway (rapid response)
• or can repress expression of the genes for all the enzymes needed for the pathway (longer-term)

Question 22

The first step of Trp biosynthesis in Arabidopsis is catalysed by

Answer 22

AS, anthranilate synthase, which is feedback inhibited by Trp.

Question 23

Post-translation modifications of proteins -

Answer 23

PTMs

Question 24

PTMs are..

Answer 24

rapid, highly regulated and highly specific. Over 300 types

Question 25

example of PTMs

Answer 25

• addition of functional groups: simple (phosphorylation), or complex (glycosylation)
• structural changes: reduction (thiol/disulphides)
• changes to an amino acid: (e.g. Gln to Glu)
• addition of proteins or peptides: ubiquitination (small regulatory
protein that can signal degradation via the proteasome, alter cellular location, activity or protein interactions), SUMOylation (Small Ubiquitin‐like Modifier) that often increases the protein lifespan and stability.

Question 26

PTMs: Proteins may undergo

Answer 26

a single type of modification or combinations of PTMs.

Question 27

Some PTMs are

Answer 27

fixed for the life of the protein (cleavage of a signal peptide or glycosylation), while other changes are reversible, such as phosphorylation.

Question 28

Post-translational modifications increase

Answer 28

protein diversity.
PTMs exponentially increase the complexity of the proteome relative to both the transcriptome and genome.
An efficient, cost‐effective mechanism for the diversification of the genome.

Question 29

Moonlighting proteins

Answer 29

Many proteins have two or more different functions.
• Some crystallins, structural proteins in the lens of the vertebrate eye, are also enzymes, e.g. duck ε‐crystallin is lactate dehydrogenase, turtle τ‐ crystallin is enolase.
• Aconitase in man is both an enzyme of the Krebs cycle and involved in iron homeostasis.

Question 30

Extended aerobic respiration requires

Answer 30

a regulated supply of carbon from glycogen and lipids

Question 31

Glycogen granule has ____ glucose units and score protein ____.

Answer 31

~30,000

glycogenin

Question 32

Glycogen is similar to _ in plants

Answer 32

amylopectin but is more branched

Question 33

branching gives glycogen two advantages:

Answer 33

• more soluble.
• the exposure of more C4 (non‐
reducing) ends means that glycogen can be both synthesized and degraded more quickly than a single starch chain with the same number of residues.

Question 34

Common PTM: Protein phosphorylation

Answer 34

twice that in mammals.

Question 35

Kinase/Phosphotase cascades are common in

Answer 35

eukaryotes and act as amplifiers

Question 36

Protein kinases make up ___ of the Arabidopsis genomes

Answer 36

~5.5%

twice that in mammals

Question 37

Control of glycogen metabolism by protein phosphorylation: Glycogen breakdown increases

Answer 37

blood Glc → Glc 1‐P → Glc 6‐P. Glc 6‐P increases the rate of glycolysis in muscle.

Question 38

Control of glycogen metabolism by protein phosphorylation: Insulin, glucagon, and epinephrine (adrenaline) are

Answer 38

hormones controlling glycogen metabolism in mammals. Glucagon and epinephrine stimulate glycogen degradation, opposing effect of insulin.

Question 39

Glucagon is a

Answer 39

a peptide hormone, is secreted by the pancreas in response to low blood Glc. An elevated glucagon concentration occurs during fasting.

Question 40

The adrenal glands release:

Answer 40

epinephrine in response to neural signals that trigger the fight‐or‐flight response (response to a sudden energy requirement).

Question 41

Glucagon and epinephrine action is selective because

Answer 41

only liver cells have receptors. Glucagon and insulin act over longer periods to maintain a relatively constant concentration of blood Glc (~5 mM).

Question 42

Diabetes: type 1

Answer 42

Type 1 diabetes develops when the pancreas is unable to produce any insulin (autoimmune disease).

Question 43

diabetes: type 2

Answer 43

Type 2 diabetes develops when the pancreas can still make some insulin, but not enough, or when insulin that is produced does not work properly (insulin resistance).

Question 44

Before discovery and purification of insulin

Answer 44

in the 1920’s diabetes was fatal.

Question 45

Insulin was the first

Answer 45

peptide drug, protein sequenced, protein structure solved, hormone measured in blood, hormone gene cloned, first recombinant and first biotech drug.

Question 46

Glycogen synthesis is regulated by protein phosphorylation: Glycogen synthase adds

Answer 46

UDP-Glc to a growing chain of glycogen. Two forms: glycogen synthase a is dephosphorylated and active. Glycogen synthase b is phosphorylated (P) by protein kinase A and is inactive.

Question 47

Glycogen synthesis is regulated by protein phosphorylation: Protein kinase A is activated by

Answer 47

Protein kinase A (cyclic AMP‐dependent protein kinase A) is activated by a messenger, cyclic AMP (cAMP). The binding of epinephrine (adrenaline) or of glucagon to liver cell G‐protein linked receptors activates the adenylyl cyclase pathway which forms cAMP.

Question 48

Kinase/ phosphatase cascades regulate glycogen metabolism:

Glycogen phosphorylase a is

Answer 48

active phosphorylated form of the enzyme that degrades glycogen. Glycogen phosphorylase b is the dephosphorylated inactive form.

Question 49

Kinase/ phosphatase cascades regulate glycogen metabolism:

glycogen synthase and glycogen degradation have a

Answer 49

Reciprocal relationship of the glycogen synthase (inactive) and glycogen degradation enzymes (active).

Question 50

Kinase/ phosphatase cascades regulate glycogen metabolism:

Phosphorylase kinase phosphorylates

Answer 50

Phosphorylase kinase phosphorylates glycogen phosphorylase. Phosphorylase kinase is activated by phosphorylation by protein kinase A. Thus, epinephrine and glucagon will stimulate glycogen degradation in addition to switching off glycogen synthesis.

Question 51

The kinase cascade amplifies the

Answer 51

Signal.
Each successive element in the pathway, once activated, can act on many molecules of its substrate (next molecule in the cascade). This amplifies the signal and greatly increases the rate of glycogen mobilisation.

Question 52

Insulin reverses

Answer 52

he effects of glucagon and epinephrine and stimulates glycogen synthesis in the liver

Question 53

Insulin is synthesised

Answer 53

in the pancreas after feeding when blood glucose increases. High [Glc] lead to storage of carbohydrate as glycogen.

Question 54

Effect of insulin is the opposite to

Answer 54

glucagon and epinephrine. Insulin binds to a cell surface receptor and triggers a pathway that leads to activation of protein phosphatase‐1. Dephosphorylation of three enzymes leads to inactivation of glycogen degradation and activation of glycogen synthesis.