MGD S3 - Protein activity regulation, Chromosomes, DNA and Nucleotides Flashcards Preview

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Flashcards in MGD S3 - Protein activity regulation, Chromosomes, DNA and Nucleotides Deck (52):

What is Allosteric enzyme control and what kind of enzymes does it control?

Activator or inhibitor binds to one subunit to either enhance or inhibition started binding to other sites

Activators increase proportion of enzyme in the high affinity R state

Inhibitors increase the proportion of enzyme in the low affinity T state

Controls multisubunit enzymes


Describe covalent modification of enzymes.
What is the most important modification made and why?

Additional groups covalently bound to amino acids in the chain.

Phosphate groups bound by kinase or removed via phosphatase.

This is important because phosphate group are charged and large, which can have a great effect on enzyme activity/conformation.


What is Proteolytic activation?

Cleavage of a protein (E.g. Inactive precursor such as a zymogen) by a protease enzyme to activate when required.


List the major regulatory mechanisms that control enzyme activity.

Allosteric control
Substrate or product conc
Covalent modification
Proteolytic activation
Regulation of enzyme amount (synthesis vs degradation)


What enzyme controls the rate determining step of glycolysis and what is the major factor in its regulation?


Allosteric control


What are phosphofructokinase inhibitors and what effect does this have on its substrate affinity?

ATP, citrate, H+
Shifts affinity curve to the right hence decreasing affinity.


What are phosphofructokinase's activators and what effect does this have on it's substrate affinity?

AMP, fructose-2,6-biphosphate
Shifts affinity curve to the left, hence increased affinity.


What is an enzyme cascade?

A chain of enzymes that activate other enzymes.


What is the function of kinase enzymes?

Kinase enzymes transfer a phosphate from ATP to the -OH group of Ser, Tyr or Thr


List some zymogens, their post cleavage enzymes and where they're found.

Pepsinogen --> pepsin

Chymotrypsinogen --> chymotrypsin
Trypsinogen --> trypsin
Procarboxypeptidase --> carboxypeptidase
Proelastase --> elastase


Name the purine bases and give a short description of their general structure.

Guanine, adenosine

Two ring structure


Name the pyrimidine bases and give a short description of their general structure.

Thymine, cytosine, uracil

One ring structures


What is a base pair?
List the base pairs found in DNA or RNA

Hydrogen bonded pair of bases, one purine, one pyrimidine


How are DNA/RNA strands labelled?

From 5' to 3' where 5' is the phosphate end (phosphate on carbon 5) and 3' is the hydroxy end (-OH group on carbon 3)


When labelling drawn out antiparallel DNA strands, which strands is labelled 5' - 3' and which strand is 3'- 5'?
When both strands are drawn out like this, it is called a...?

Top strand = 5' - 3'Lower strand = 3' - 5'

Duplex structure


What are Histones and how do they relate to DNA?

Histones are proteins that DNA strands wrap around (2 wraps per histone molecule).


What is a DNA/Histone complex called?



How are nucleosomes further compacted?

Nucleosomes wrapped into a solenoid structure


During mitosis what form do chromosomes take and what can be said about gene function during mitosis?

Chromosomes densely packed in short fat fibres. No gene expression or replication.


During interphase what form do chromosomes take and what can be said about gene function during interphase?

Chromosomes decondensed (beads on a string) and genome will express and replicate.


How are polynucleotide chains linked?

Covalent phosphodiester bonds


Are DNA/RNA chains polar?



Base pairing is what type of bonding?

Hydrogen bonds


Base pair bonding occurs between what two groups?

Oxygen (electronegative)
Nitrogen/hydrogen (positive)


How many bonds are present between the base pairings?

AT = 2
CG = 3


What is an RNA stem loop structure?

Single RNA chain folds and complementary base pairs on the same chain form bonds.


Describe the key features of the DNA double helix.

Two independent, anti parallel and complimentary polymers
One turn is 10 base pairs
0.34nm between base pairs
Bases unsaturated and planar
Major (exposed bases) and minor grooves


Name the stages of DNA replication



Explain the process of initiation during DNA replication

Helicase unravels DNA polymer from 3' to 5'
Primase interacts with DNA strands at specific initiation sites
Primase recruits DNA polymerase


Explain the process of elongation in DNA replication

Leading strand duplicated by DNA polymerase in continuous fashion
Lagging strand replicated discontinuously to form Okazaki fragments
Fragments bound covalently by DNA ligase (between -OH and phosphate groups)


Explain the process of termination in DNA replication

Replicating strands that were initiated at different sites move towards each other, leading towards lagging strand and vice versa. Once they meet DNA ligase joins the strands.


Describe the necessary substrates/precursors required for DNA polymerase to function

Requires activated dNTP (deoxyribonucleosidetriphosphates)
Eg. dATP, dGTP, dCTP, dTTP

Driven by hydrolysis of ATP


DNA polymerase forms new chains in what direction?

5' to 3'


Describe the function of Helicase enzymes

Unzips DNA from 3' to 5' the site where Helicase is working is known as the replication fork

Requires ATP


How are changes in total amount of an enzyme regulated?

Regulation of enzyme synthesis:

Increases or decreases depending on rate of transcription of mRNA

Regulated protein degradation:

Enzymes can be tagged for destruction by the addition of a small protein molecule known as ubiquitin


Describe the 3 methods of metabolic pathway regulation?

Feedback inhibition:

End product of pathway inhibits enzymes earlier in the pathway, hence inhibiting its own production

Feedforward activation:

Increased amount of substrate increases the rate of the first step of the pathway

Counter regulation:

Activation of catabolic pathways will inhibit the opposing anabolic pathway and vice versa.


What are the 5 methods of regulation of the blood clotting cascade?

Inactive zymogens present in low concentration

Amplification of initial signal

Localisation of clotting factors to the site of damage

Feedback activation of thrombin

Termination of clotting by multiple processes


Describe how the concentration of inactive zymogens is a factor in the control of the blood clotting cascade.

Most tissue factors present in low concentration to ensure that clotting is not accidentally initiated.

Zymogen dilution at the damaged site via blood flow and removal by the liver inhibits clot formation.


Describe how amplification of the initial signal is active in the regulation of the blood clotting cascade

Damage to blood vessels initiates cascade of activation resulting in the formation of an insoluble blood clot


How is the localisation of clotting factors at the site of damage a factor in the regulation of the blood clotting cascade?

Factors with Gla domains bind to Ca2+ ions on the damaged endothelial cell lining and allow rapid activation of the downstream effector molecules


How is feedback activation of thrombin a factor in the regulation of the blood clotting cascade?

Activated thrombin enhances the conversions of Factor V, VIII and XI to activated forms


How is the termination of clotting carried out?

Clotting is stopped by the removal of activated proteins, proteolytic digestion and the binding of inhibitor molecules


In the fibrin clot cascade what is the intrinsic pathway?

Damaged blood cell membranes promote the binding of factor 11 initiating an enzyme cascade.


In the fibrin clot cascade what is the extrinsic pathway?

Damaged tissues release factor 3 which initiates an enzyme cascade.


What is the result of thrombin activation?

Cleaves fibrinogen to form fibrin


How does protein C affect clotting?

Some clotting factors are degraded by protein C, inhibiting clot formation.


What is heparin's role in clotting?

Heparin enhances the inhibitory effect of antithrombin III on thrombin and hence is a cofactor to AT3


Define Fibrinolysis

Clot Breakdown


What enzyme is responsible for fibrin breakdown, additionally, what is it's Zymogen and how is it activated?

Streptokinase and t-Pa


What are Gla domains and where are they found?

How are they formed?

Gla domains are regions of clotting factors rich in carboxyglutamate residues

They're found in clotting factor II, VII, IX and X

Formed via carboxylation of glutamate residues in a vitamin K regulated process in the liver


Describe the structure of Fibrin

Contains 2 sets of 3 polypeptides (alpha beta and gamma chains) joined at the N termini by disulphide bonds

Each set contains 3 globular domains joined by rods

N-terminal regions of the alpha and beta chains are highly negatively charged and prevent aggregation of fibrin


How is fibrin activated?

What happens to activated fibrin?

Fibrin is activated when the highly negative N terminal regions of the alpha and beta chains are cleaved off by thrombin

The C terminal ends of the beta and gamma chains then interact with exposed sequences of the N-termini of the cleaved alpha and beta chains to form a fibrin mesh/clot