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What is a motif?

A polypeptide with o folding pattern that contains one or more elements of secondary structure
e.g. Beta barrel or beta-alpha-beta loop.


What is a domain?

Part of a polypeptide chain folding into a specific shape.


What are the 5 types of interactions possible in a protein?

H bonds
Van der waals
Ionic bonds
Hydrophobic interactions
Disulphide bonds


What decides a molecules solubility?

It's ability to form H bonds.


What are the essential amino acids?

Tryptophan, valine, leucine, lysine, isoleucine, phenylalanine, methionine, threonine.


Describe a beta pleated sheet.

0.35nm between amino acids.
Variable groups alternate on each side.
Strands arrange parallel and form H bonds.


Describe an alpha helix.

3.6 amino acids per turn
0.54nm pitch
Right handed helix
H binds parallel to helix
R groups on outside of helix.


What amino acids are helix breakers and why?

Proline - has a ring structure therefore lacks rotation around the N-C bond

Glycine - R group supports other conformations.


What amino acid is a helix former?

Alanine - it has a small hydrophobic side chain


What are the structures of proteins?

Primary - linear amino acid sequence
Secondary - local spatial arrangement of polypeptide backbone
Tertiary - 3D arrangement of atoms in the polypeptide
Quaternary - 3D arrangement of protein subunits.


What are amyloidoses?

Aggregations of misfolded proteins that therefore become insoluble.
They have a degree of beta pleated sheet and are stabilised by hydrophobic interactions between hydrophobic residues.


What drives folding?

Mostly the hydrophobic effect.


How are some proteins aided with folding?

By chaperones.


What are the features of peptide bonds?

Trans conformation
No rotation
All atoms of the bond are in the same plane


What are globular proteins?

They're involved in catalysis and regulation.
Have several types of secondary structure.
e.g. Hb


What are fibrous proteins?

For support, shape and protection.
Form strands or sheets.
Have one type of repeating secondary structure.
e.g. collagen


What are the features of Hb?

Found in the blood.
Carries O2 and CO2.
Has 4 haem groups.
Is tetrametric.


What are the features of myoglobin?

Stored in muscle for periods of high metabolic activity
Has 1 haem group
Formed from one subunit.


How does foetal Hb differ from normal Hb?

It has a higher affinity (so curve is further left)
Is formed from 2 alpha and 2 gamma chains.


What states do Hb exist in and how does the binding of O2 affect these?

T state - tense = low affinity
R state - relaxed = high affinity

Binding of O2 stabilises the R state


What gives the sigmoidal curve for Hb?

Transition between the R and T states (= cooperativity of oxygen)


What is myoglobin s affinity for O2?

Very high, so will only release at very low pO2.


How does cooperativity work in Hb?

When an oxygen binds to the haem group, it pulls the iron atom into the plane of the ring, changing Hb conformation and making it easier for O2 to bind.


What is the Bohr effect?

The binding of H+ or CO2 lowers Hb affinity for O2 and shifts the curve to the right.

More H+/CO2 = more resp = more O2 needs releasing more readily.


What effect does CO have on Hb?

It binds 250x more readily than O2 = fatal when >50%

Increases the oxygen affinity of Hb left


What effect does 2,3-bisphosphoglycerate have on Hb and why is this good?

It decreases Hb affinity and shifts the curve right.

2,3BPG produced in metabolism so more 2,3BPG = more resp = O2 needs releasing more readily.

2,3BPG increases in concentration at high altitudes where pO2 is less = promotes O2 release.


What is sickle cell disease!

In the beta chain of Hb, negative glutamate is substituted for a neutral valine
= valine residues form a hydrophobic pocket and deform RBCs, causing them to struggle to hold O2 and to lyse easier.


What is alpha chain thalassaemia?

It is a lack of alpha subunits.
Onset before birth.
Less severe as the excess beta chains form stable tetramers with an increased affinity for Hb.


What is beta chain thalassaemia?

Lack of beta chain subunits.
Onset after birth.
More severe as the alpha chains don't form stable tetramers and instead precipitate = make RBC fragile, leading to premature death of cells.


What are the classifications of amino acids and what are the main amino acids in?

1). Negatively charged - glutamate
2). Non polar aliphatic - valine, leucine, methionine, isoleucine.
3). Aromatic R group - tryptophan, phenylalanine
4). Positively charged - lysine
5). Polar neutral - threonine


Why do active sites contain a cleft?

It excludes water to allow adsorption of the substrate.


What are the key features of enzymes?

May require cofactors
Don't effect the equilibrium
Unchanged after the reaction


How do enzymes work?

They lower the activation energy required to start the reaction by facilitating the formation of a transition state = increase rate of reaction.


What occurs in irreversible inhibition of enzymes?

The inhibitor binds tightly to the active site via covalent bonds = can't be displaced.


What are the ways in which an enzyme can be reversibly inhibited?

1). Competitively - the inhibitor binds to the enzymes active site via weak bonds.

2). Non competitively - the inhibitor binds at a place other than the enzymes active site, causing a conformational change in the enzymes shape = substrate no longer fits.


What is V0 and the equation for it?

The initial rate of the reaction, the only time where we know the substrate conc.

Vmax [substrate]
V0 = --------------------
Km + [substrate]


What is Vmax and its units?

The maximal rate the reaction can reach when all enzymes carve sites are saturated.

Measured in rate (e.g. mol/min)


What is Km and its units?

The substrate concentration at half the Vmax

M (michaelis constant) - measured in units of conc


How does Km link to affinity?

Low Km = high affinity
High Km = low affinity


How is Km and Vmax affected in competitive inhibition?

Vmax is unaffected as it can be overcome by increasing the substrate conc.

Km is increased as the inhibitor is competing with the substrate = decreases enzymes affinity.


How are Vmax and Km affected in non competitive inhibition?

Vmax decreases as substrate can no longer bind properly.

Km is unaffected as the inhibitor doesn't effect the binding of the substrate.


What is one unit in terms of enzyme kinetics?

It is the amount of enzyme that converts 1umol of substrate into product per minute under standard conditions.


What is the a Lineweaver-Burke plot and what is its purpose?

Arrangement of Michaelis-Menten equation to give a linear plot.

To allow easy estimation of Vmax and Km


What is a Lineweaver-Burke plot arranged like?

x axis = 1/[s] (substrate)

y axis = 1/[v] (rate)

x intercept = -1/Km

y intercept = 1/Vmax

slope = Km/Vmax


How are enzymes regulated in long term?

By changing the rate of protein synthesis or degradation.


What are isoenzymes and an example?

They are different forms of the same enzyme with different amino acids sequence and usually different kinetic properties.
e.g. Glucokinase in liver (switched on/off) and hexokinase (switched on)


What is substrate and product concentration regulation and an example?

The substrate availability affects the rate of enzyme activity.

e.g. Hexokinase is regulated by product G6P


What is covalent modification regulation and an example?

This is phosphorylation -
1). Kinases - Adding the phosphate group from ATP onto the OH group of a Ser, Tyr, Thr (often in cascades)
= makes the enzyme charged and bulky.

2). Phosphatases - removing a phosphate via hydrolysis.

e.g. Pyruvate kinase is dephosphorylated to activate.


What is proteolytic cleavage regulation and an example?

Activates enzymes produced as precursors/zymogens in biological systems by removing part of it.

e.g. Trypsinogen ---> trypsin.


What is allosteric regulation and an example?

Activators or inhibitors bind to multi-subunit enzymes as these have an R state and a T state (so show a sigmoidal curve rather than usual rectangular hyperbola).

Activators increase proportion of enzyme in R state.
Inhibitors increase proportion if enzyme in T state.

e.g. Phosphofructokinase is activated by AMP and fructose-2,6-bisphosphate and inhibited by ATP, citrate and H+.


How does trypsin control digestion and how is it regulated?

Cleaved by enteropeptidase from trypsinogen and activates production of all other pancreatic digestive enzymes.

Regulated by anti-trypsin.


What happens if someone is deficient in anti-trypsin?

If this is deficient, emphysema occurs (production of elastase continually activated).


What are the pancreatic enzymes?



Describe the intrinsic pathway.

Activated platelets or collagen come from damage to the endothelial lining of blood capillaries and activate conversion of factor 12 to 12a.
Cascade of reactions that include factor 8a and are stimulated by thrombin, end in production of factor 10a.
This activates prothrombin to become thrombin.
Thrombin causes fibrinogen to change to fibrin.


Describe the extrinsic pathway?

Trauma releases factor 3, which changes factor 7 to 7a.
7a changes 10 to 10a which activates thrombin from prothrombin.
Thrombin causes fibrin to form from fibrinogen.


How is prothrombin converted to thrombin?

Prothrombin has thrombin in the C terminal, then Gla (target) and Kringle (keep inactive) domains.
2 proteolytic cleavages give fully active thrombin.


What is the structure of thrombin?

2 chains held by disulphide bonds.
Contains Gla residues which are carboxylated (COOH) to give them negative charge.
This attracts them to the Ca2+ that are surrounding the damage to the membrane = cascade activated here.


What is the structure of fibrinogen?

2 sets of alpha, beta and gamma tripeptides held by disulphide bonds at the negatively charged N termini.


How is fibrinogen activated?

Thrombin cleaves the negative stalks from the N termini of alpha and beta chains = globular domains of C termini of beta and gamma chains can form a fibrin mesh = CLOT


How is a clot stabilised?

Amide bonds form between lysine and glutamine residues.


How is clotting regulated?

Inhibitors such as anti thrombin bind to thrombin and inactivate it before transporting it to the liver to be broken down.
This is enhanced by heparin.


How can clotting be stopped?

1). Localisation of thrombin - dilute the clotting factors with blood flow then remove via liver.

2). Digestion of factors by proteases - Protein C is activated by thrombin binding to thrombomodulin (an endothelial receptor) and digests factors.

3). Fibrinolysis - plasminogen is converted to plasmin by streptokinase or tissue plasminogen activator. Plasmin then breaks the fibrin into fragments.


How are proteins imported into the mitochondrial matrix?

Signal is an ampiphatic helix at the N terminus which binds to a receptor. The unfolded protein (held by chaperones using ATP) is then passed through the TomTim transporter. The signal is then cleaved and the chaperones dissociate.
The protein also has positive residues, which are attracted to the negatively charged mitochondrial matrix.


How is protein imported into the nucleus?

Signal is a sequence of 5 basic amino acids. These are recognised by, and therefore bind to importin, allowing them to move into the nucleus. Here, ran-GTP binds, and the protein is released.
Importin and ran-GTP are both recycled to the cytosol where the GTP is hydrolysed and ran transported back to the nucleus.


How are proteins imported into the peroxisomes?

Signal is a peroxide enzyme sequence (usually Ser-Lys-Leu) which binds to a receptor. This receptor forms a part of a translocator. The protein therefore dissociates into the peroxisome and ATP recycles the receptor.


Which ribosomes remain cytosolic?

Those producing proteins not destined for secretion (often targeted at organelles).


How do proteins destined for secretion enter the ER?

1). A free ribosome initiates protein synthesis.
2). The hydrophobic signal sequence of the polypeptide protrudes at the N termini from the ribosome = is recognised by SRP so SRP binds.
3). GTP bound SRP and the ribosome then bind to an SRP receptor on the cytosolic face of the ER membrane.
4). Binding of the ribosome causes protein translocator channels to open and the hydrolysis of GTP allows the protein to enter the ER.
5). The hydrophobic signal is cleaved by signal peptidase and continues to enter the ER until the ribosome reaches a stop codon.


How are membrane proteins made?

1). A free ribosome initiates protein synthesis.
2). The hydrophobic signal sequence of the polypeptide protrudes at the N termini from the ribosome = is recognised by SRP so SRP binds to it.
3). GTP bound SRP and the ribosome then bind to an SRP receptor on the cytosolic face of the ER membrane.
4). Binding of the ribosome causes protein translocator channels to open and the hydrolysis of GTP allows the protein to enter the ER.
5). A second hydrophobic sequence is reached in the translocator, known as a stop transfer anchor sequence.
6). Protein synthesis now occurs on the cytoplasmic face of the ER until a stop codon is reached.


How are proteins sent from the Golgi to lysosomes?

1). Attachment of phosphate groups to the OH groups of mannose sugars (using 2 enzymes = mannose 6 phosphate) on the lysosomal hydrolases.
2). M6P is detected by M6P receptors on the trans Golgi and the vesicle is then sent to the lysosomes.
3). The acidic pH at the lysosomes then causes dissociation of the protein and transporter.
4). Transporter is recycled.


What is the effect of missing the enzyme involved in attaching phosphate groups to OH groups of mannose sugars in lysosomal hydrolases?

I cell disease - hydrolases become present in the blood and the lysosomes bloat as they can't digest what the ingest.


What modifications can occur in the Golgi?

1). Trimming and modification of N linked oligosaccharides.

2). Further processing of some proteins.

3). O linked glycosylation


What is O linked glycosylation?

The attachment of sugar to OH groups, usually of Ser and Thr.
It requires glycosyl transferase and is important for proteoglycans.


What are proteoglycans found in?

The ECM and mucus.


What modifications occur in the ER?

1). Signal cleavage via signal peptidase

2). The conversion of proline from cis to trans form to aid folding by peptidyl-prolyl-isomerases.

3). Formation of disulphide bonds.

4). N linked glycosylation.


What occurs in N linked glycosylation?

The oligosaccharide is made in a lipid carrier molecule called dolichol phosphate and inserts into the membrane.
Sugars are added to the amino group of asparagine
(In a specific motif?)


What is the importance of N linked glycosylation?

It increases the proteins half life
It aids in correct folding
It allows interaction with other molecules


How are disulphide bonds formed in the ER?

Protein disulphide isomerase transfers the electron from the SH group to itself = SS bond can form = disulphide bond.


How do enzymes meant to be in the ER such as PDI not secreted?

They have a KDEL signal at their C terminus.
If secreted, the Golgi contains KDEL receptors and repackage the protein to return it to the ER.
The protein is released at a higher pH so is released at the ER rather than Golgi.
PDI dissociates from the receptor in a neutral condition and the KDEL receptor is recycled.


What happens of misfolding occurs during modification?

Chaperones bind and will monitor the extent of misfolding or retain the protein in the ER. They can then mediate the increased transcription of chaperones or a reduction of translation of the protein.


What are general results of protein misfolding?

Toxic accumulation of the protein in the ER.
Protein degraded in the cytosol.


How is insulin secreted?

Regulatory secretion.


How is insulin made?

Preproinsulin is cleaved to proinsulin.
PDI forms 3 disulphide bonds between the 2 chains.
In the vesicle after processing by the Golgi, endoproteases cleave the C peptide = mature insulin and C peptide secreted together.


What are some features of the structure of collagen?

Every 3rd amino acids is a glycine.
Most of the 1st amino acids will be proline.
Forms a right handed triple helix.
3 chains of 300nm rods.


How is collagen partially synthesised in the ER?

1). Preprocollagen is synthesised into the ER lumen then cleaved to procollagen.
2). Prolyl hydroxylase adds OH groups to many proline residues.
3). N-linked oligosaccharides are attached to the propeptide sections (NOT where the helix will form).
4). Alpha chains align and form disulphide bonds via PDI = formation of triple helical procollagen from C to N terminus.


What are the cofactors of prolyl hydroxylase?

Vitamin C and Fe2+


How is collagen synthesis completed after the Golgi?

1). Vesicles containing procollagen bud off from the trans face of the cisternae and leave the cell via exocytosis.
2). The C and N terminal peptides are removed via procollagen peptidase.
3). Tropocollagen units form covalent bonds via the extra cellular enzyme lysyl oxidase = cross linking = collagen fibrils!


What deficiency causes Ehlers-Danlos syndrome?

A deficiency in lysyl oxidase.


Why do we have proteolytic processing?

1). Some enzymes would be destructive if activated in the cell.
2). Can yield different products from the same precursor by processing it in different areas which contain different enzymes.
3). Can give products that would otherwise be too small to enter the ER.


What can phosphorylation do to an enzyme?

Activate or inactivate it.


Why are babies given Vit K at birth?

The body can't produce it naturally and relies on bacteria in the gut to produce it = not born with these. Milk doesn't contain enough.


What is found at the 5' and 3' end of a strand of DNA?

5' = free phosphate
3' = free OH


How is DNA organised in cells and why is this important?

DNA is wrapped around histones, around chromatin, which form "beads on a string" (nucleosomes). The nucleosomes pack tightly to form solenoid fibres which are the decondensed form of a chromosome.

This is important as it ensures all DNA fits in the cell without being damaged. The level of condensation regulates gene expression and is important in mitosis.


What is a nucleoside and a nucleotide?

Nucleotide - ribose, phosphate and base.

Nucleoside - ribose and base


How do glucokinase and hexokinase differ in terms of Km and how is this helpful?

Hexokinase has a lower Km. This means it is usually active. Glucokinase has a much higher Km, so will only be activated at high glucose levels, when the hexokinase is being "swamped". Glucokinase also isn't inhibited by G6P


What tissues are dependant on glucose?

Kidney medulla


What letter can you give the wobble position?



What are restriction endonucleases?

Restriction enzymes from bacteria that recognise specific palindromic sequences.