MGD Flashcards
When pH>pK which form of an acid forms the dominant?
De protonated
Define pK
The stronger the tendency of an acid to dissociate, the lower the pK value
When pH<pK which for of an acid takes the dominant?
Protonated
What are the 3 classes of amino acids based upon charge?
Nonpolar hydrophobic
Polar, uncharged, hydrophilic,
Polar, charged, hydrophilic,
What are the 2 classes of amino acids based upon structure? Give an example of each
Ring = Aromatic eg tyrosine
Without a ring = aliphatic eg lysine
Give 2 examples of positively charged amino acids.
Lysine, Arginine, Histadine.
Give 2 examples of negatively charged amino acids.
Aspartate, glutamate.
Give an example of a non polar amino acid.
Valine
Give an example of a polar, uncharged amino acid.
Serine
Define pI
The isoelectric point
pH at which the protein has no overall charge.
Which type of charge is dominant in amino acids making up an acidic protein?
Negative. Low pI
Which type of charge is dominant in amino acids that form a basic protein?
Positive. High pI
What type of bond forms between two amino acids?
Peptide bond
When drawing a polypeptide, what orientation is it drawn?
Trans, hence Carbonyl O and amine H are on opposite sides.
What is an amyloidose?
Improper folding of tertiary structure of proteins.
What is the name when the polypeptides are the same in quarternary strucure?
Homomeric
What is the name when the polypeptides are different in quarternary strucure?
Heterogenous
What type of structure is found in fibrous proteins?
Repeating primary structure.
What types of proteins have several secondary folding structures?
Globular
What is the pitch and number of amino acids per turn of an alpha helix of a polypeptide. Which direction does it turn?
0.54nm
3.6 amino acids per turn
Right hand
What type of amino acid acts as a helix fixer? Eg?
Small hydrophobic amino acids, eg Ala + Leu
Which two amino acids act as helix breakers and why?
Pro - no rotation around N-C
Gly - small R group supports other conformations
What are the two states of deoxyhaemoglobin? Which has the higher affinity for oxygen?
The tense and relaxed state.
R state has a higher affinity for oxygen
What is the full name for BPG?
2,3 bisphosphoglycerate.
What does BPG do to haemoglobin. Curve effect?
Decreases its affinity for oxygen, curve shifts to the right.
Describe the Bohr effect.
CO2 and H+ causes the affinity of haemoglobin to decrease, hence curve shifts to the right.
More offload of oxygen at actively restoring tissues.
What inheritance pattern is displayed by sickle cell anaemia?
Autosomal recessive
What substitution of amino acids is made in sickle cell anaemia?
Glutamate to Valine
Why does the substitution of glutamate to valine cause sickle cell anaemia?
Valine is hydrophobic and sits on the outcode of the cell. Hence Hb polymerises and forms a sickle shape.
What problems are caused by sickle cell anaemia?
Blockage of micro vascular
Premature lysis of RBC leading to anaemia and jaundice.
Describe alpha thalassaemias
A decrease or absence of alpha polypeptide chans in Hb
Beta chains form stable terameters with increased affinity for oxygen
Onset before birth
Describe beta thalassaemias.
A decrease or absence of beta polypeptide chains in Hb.
Alpha chains cannot form stable tetramers
Symptoms appear after birth.
How do enzymes catalyse reactions?
Provide a lower activation energy by:
Increasing local concentration of reactants.
Stabilise the formation of the high energy transition state.
What is the Michaelis-Menton equation?
Vmax x [S] / Km + [S]
What does Vmax stand for?
The maximum rate of reaction when the enzymes are saturated with a substrate.
What does Km stand for?
The concentration of a substrate that gives 1/2 Vmax
The Michaelis constant.
What effect does non-competitive inhibiton have on Km and Vmax?
Reaction will not reach Vmax
No change to Km
What effect does competitive inhibition have on Vmax and Km?
How is this overcome?
Km increases
No effect on Vmax
Can be over come by adding more substrate
Describe allosteric modification.
Enzymes with more then 1 subunit, when substrate is bound to one active site, then this will enhance/disrupt substrate binding at another active site.
Give an example of allosteric inhibition and activation in glycolysis.
Phosphofructo kinase is:
Activated by AMP
Inhibited by ATP, citrate and H+
Describe the main method of covalent modification of enzymes.
A large, charged phosphate group is added to an amino acid in the protein, hence disrupting its structure.
Added by kinase enzymes
Removed by phosphotase enzymes.
Describe proteolytic activation of enzymes.
Enzymes are secreted as inactive precursors (zymogens).
These enzymes are cleaved by protease enzymes to activate them.
Define a zymogen.
An inactive precursor enzyme.
Describe an enzyme cascade.
When enzymes activate other enzymes, ie activation of zymogens.
What is the precursor of pepsin?
Pepsinogen
What is the enzyme formed from trypsinogen?
Trypsin
What is the precursor enzyme of elastase?
Proelastase
What factor is activated by the intrinsic pathway of the clotting cascade?
Factor XII
What factor is activated by the external pathway of the clotting cascade?
Factor III
What is the first factor that the intrinsic and extrinsic pathways of the clotting cascade have in common?
Factor X
What zymogen is activated by factor X in the clotting cascade and hence what enzyme is formed?
Prothrombin to Thrombin
What zymogen is activated by Thrombin in the clotting cascade and hence what enzyme is formed?
Fibrinogen to fibrin
What enzyme provides positive feedback in the clotting cascade?
Thrombin
How does fibrin produce a clot?
It forms a fibrin mesh, as father cleavage globular domains are exposed and so bind together. Cross linking then occurs between the polymers between lysine and glutamine
Which factor has a defect in haemophilia a?
Factor VIII
What are the methods of regulation in the clotting cascade?
Inactive zymogens at low concentration.
Enzyme cascade.
Localisation of clotting.
Feedback by thrombin
What is the relevance of Gla and Ca2+ in the clotting cascade?
Some glutamate in factors have a carboxyl group added to them. This will bind to Ca2+. Ca2+ binds to platelets, ie the area of damage. Hence localisation of the factors.
How is the clotting cascade stopped, and the clot removed?
Dilution of clotting factors by blood flow and the liver.
Anti thrombin III is activated by heparin.
Protein C is activated by thrombin binding to endothelial receptors. This protein degrades factors by stimulating proteases hence fibrinolytic.
How many rings do purines have?
2
How many rings does pyrimadines have?
1
What are the purine bases?
Adenine and guanine.
What are the pyrimadines?
Cytosine, Thymine and Uracil.
What nucleotide base binds to Adenine? How many hydrogen bonds are formed?
Thymine, 2
What nucleotide base binds to Guanine? How many hydrogen bonds are formed?
Cytosine, 3
How many hydrogen bonds between Cytosine and Guanine?
3
How many hydrogen binds between adenine and thymine?
2
What group is free at the 5’ end of a DNA helix?
Phosphate
What group is free at the 3’ end of a DNA helix?
Hydroxyl
What type of bond is formed between nucleotides?
Phosphodiester bonds
What is an RNA stem loop?
When RNA loops back on itself and hydrogen bonds form between complimentary bases, hence 1 strand is anti parallel to the other eg tRNA
What is the pitch of DNA double helix?
0.34nm
How many base pairs make up a full revolution of a DNA helix?
10
What is the significance if purines and pyrimadines being planar and unsaturated?
They can lie ontop of each other well ie less space required in the DNA helix
What are the two grooves in a DNA helix?
Major and minor
Describe a nucleosome.
DNA wound around a charged his tone core.
Describe a solenoid.
Nucleosome a coiled to form solenoid structures.
Which form of chromosome is condensed and the genome is not expressed, hence it can’t be replicated?
Mitotic chromosome.
Which form of the chromosome is decondensed, the genome is expressed and so can be replicated?
Interphase chromosome (chromatin)
Describe the three main processes of initiation of DNA replication.
Recognition of an origin of replication.
DNA is unravelled by helicase.
Primase forms a primer of dNTPs.
What is the full name of dNTPs?
Deoxyribonucleic triphosphate.
What occurs in the elongation stage of DNA replication?
DNA polymerase adds dNTPs to an already existing chain.
In which direction does DNA polymerase form new Polynucleotides? What is the name of the segments that are formed due to this?
5’ to 3’
Okazaki fragments.
What enzyme binds Okazaki fragments together?
DNA ligase.
What is the name of the polynucleotide strand comprised of Okazaki fragments?
The lagging strand.
What is required for DNA polymerase, DNA primate, DNA ligase and DNA helicase all to work?
ATP
What enzyme recoils the polynucleotide chains after DNA replication has occurred?
Helicase
What occurs the the phase G1
Cell growth
What occurs in the S phase of a cell?
Replication of DNA
What occurs in the G2 phase of a cell?
Checking of polynucleotide sequences, preparation to divide.
What occurs in the M stage of a cell?
Cell division.
