3 Protein Regulation/ DNA Structure Flashcards
3.2 What are the allosteric properties of a key regulation enzyme?
They show sigmoidal relationships between rate and [substrate] due to having a T state (low affinity from inhibitors) and an R state (low affinity from activators).
These enzymes have no Km due to the sigmoidal graphs
Allosteric activators/ inhibitors do not bind to the active site of enzymes.
E.G. Phosphofructokinase (F6P, ATP -> F16BP, ADP) is activated by AMP, F26BP and inhibited by ATP, citrate and H+.
3.1 what are the regulatory mechanisms that control enzyme activities? Give examples
Short term:
1) Substrate & product concentration e.g. Fixed NAD/ NADH concentration. Accumulation of product can limit the forward reaction.
2) Enzyme conformation such as covalent modification, allosteric inhibition/ activation and proteolytic cleavage.
Long term:
1) change in rate of synthesis via enzyme induction/ repression.
2) change in rate of degradation through using molecules such as ubiquitin which attached to proteins and signals their degredation. Also through proteasome pathways.
3.3 What is the concept enzyme cascades and the use of protein kinases and phosphatases to regulate activity?
These are methods of covalent modification.
Protein kinases transfer the terminal phosphate from ATP to the -OH group of Ser, Thr and Tyr. This adds bulk to a protein and makes it negative, allowing it to form H bonds and leading to grouping of proteins which effect enzyme activity.
Protein phosphates reverse the effects of protein kinases.
The activation of one enzyme can cause other enzymes to be activated, causing other enzymes to be activated with the number of active enzymes increasing with each step. This is called the enzyme cascade.
3.4 What is a zymogen? Give examples.
A zymogen is an inactive precursor of an enzyme that can become activated via proteolytic cleavage.
Zymogens often contain extra amino acid sequences which are removed in proteolytic cleavage. This is a non reversible process.
Zymogens often end with “-ogen” or begin with “-Pro”.
Zymogens are broken down by proteases.
3.5 how does the activation of the clotting cascade lead to the formation of fibrin?
The activation of the blood clotting cascade is caused by damage to the endothelium lining promoting binding if factor XII (intrinsic pathway) or by tissue trauma releasing factor III.
The factors activate zymogens and the enzymes formed, in turn, activate other zymogens in a cascade. Most changes involve the activation of zymogens.
One of the final steps is the cascade involves prothrombin being converted to thrombin. This happens because of the Gla section that prothrombin contains. Gla is made in the liver (through the addition of COOH by vitamin k) and is found as a part of many clotting factors. It is important as it is attracted to Ca2+ found on membranes and brings clotting factors together. Gla allows prothrombin to be targeted for its activation.
Thrombin converts fibrinogen into fibrin through cleavage of highly negatively charged areas. In fibrinogen, these areas repel other fibrinogen molecules but without them, fibrin bonds to create a large mesh that can lead to a blood clot.
3.6 discuss the mechanisms involved in the regulation of clot formation and breakdown.
1) localisation of (pro) thrombin - factors are diluted by blood flow and removed by the liver.
2) factors are degraded by proteases such as protein C which is activated by thrombin binding to the membrane receptor thrombomodulin.
3) the use of specific inhibitors such as antithrombin III (AT3) which is enhanced by heparin binding
4) plasminogen also breaks down fibrin. T-PA and streptokinase cause plasminogen to convert to plasmin.
Other factors include:
Low conc of inactive zymogens, proteolytic activation, the cascade amplifying signal and feedback activation by thrombin (speeds up other steps of cascade)
3.7 recognise the structural components of DNA and RNA
DNA contains a pentose sugar 2-deoxyribose whereas RNA contains ribose.
Both DNA and RNA contain a base, sugar and phosphate group. They can join via phosphodiester bonds.
Bases are either purines (double ring) such as guanine and adenine or pyrimidines (single ring) such as uracil, thymine or cytosine.
3.8 recognise and apply the conventions used to represent DNA/ RNA base sequences.
Base sequences are represented by the letters that stand for the base type. They are written in the order they are found starting with 5’ (P end) and finishing with 3’ (OH end). Unless you are trying to show complimentary sequences.
3.9 explain polarity of a DNA/RNA chain.
Chains have polarity 5’ at P end to 3’ at OH end.
3.10 explain the importance of hydrogen bonding and base pairing in defining nucleic acid secondary structure
Complementary base pairs can form hydrogen bonds between two strands of DNA, RNA or both. This is the reason DNA is found in a helix shape as all the bridges between the two strands come from complementary base pairing. RNA often form step loops because of this where a single chain doubles back in itself due to complementary base pairing.
Guanine forms 3 H bonds with Cytosine and Uracil/Thymine forms 2 H bonds with Adenine.
3.11 describe the key features of a DNA double helix
Right ranked helix.
3.12 explain how eukaryotic DNA is condensed in nucleosomes and relate this to the structure of chromosomes.
Negatively charged DNA is wrapped around positively charged histones. 1 wrapped histone is called a nucleosome.
Nucleosomes are packed into solenoids (30nm). Solenoids wrap around themselves and twist so that the overall shape forms the chromosomes.
3.13 Show an appreciation of the vast amount of DNA found in a cell.
3,200 million genes in human DNA
