Flashcards in Macromolecules Deck (90):
What are some of the functions of carbohydrates?
1. Energy storage (e.g. glycogen)
2. Structural support (e.g. cellulose)
3. Protection (e.g. cellulose)
4. Cell signalling (e.g. glycoprotein receptors)
5. Cell adhesion
What is the most common form of glucose?
What is the reducing end of a di/polysaccharide?
End that can still be opened to form polysaccharide (e.g. for starch, the 1' end).
What is the structure of chitin?
Modified cellulose with N-acetyl glucosamine groups attached to carbon 2 on β-D-glucose.
How can carbohydrates be linked to proteins?
1. N-linked: Linked to Asn
2. O-linked: Linked to Ser or Thr
What is a glycosidic bond?
Bond between a sugar and any other compound.
What are the non-polar amino acids?
What are the polar amino acids with uncharged R-groups?
What are the polar amino acids with charged R-groups?
4. Aspartic acid
5. Glutamic acid
Which amino acid can form disulfide bonds?
Which amino acids are capable of being phosphorylated?
What is the chirality of all naturally occuring amino acids?
How are amino acid comparable to the glyceraldehyde in the Fischer convention?
Amino group = Hydroxyl group
Carboxyl group = Aldehyde group
R group = CH2OH
H = H
What is the experiment that showed proteins are capable of self-folding?
1. A sample of RNAse is obtained.
2. Metcaptoethanol is used to break disulfide bonds.
3. Urea is used to disrupt electrostatic interactions.
4. Once denaturing agents are removed, protein refolds by itself and is active.
What are the conditions that dictate the secondary structure of proteins?
1. Optimum length (2.5 Å) and linearity of hydrogen bonds.
2. Amino acids are oriented to avoid steric clashes.
Why is the peptide bond rigid?
Because electron from C=O bond capable of delocalising, into peptide bond, resulting in it having 40% double bond properties.
What are the angles of rotations about an α-carbon?
- ɸ is the angle between α-carbon and N.
- Ψ is the angle between α-carbon and C.
What are the properties of an α-helix?
- The helix is right-handed.
- R-groups are pointing outwards from the helix.
- The C=O on the N-terminus residue (i) makes H-bond with N-H on i+4 residue.
- There's 3.6 residues per turn.
- Each turn rises 5.4Å.
What types of interactions hold tertiary structures together?
1. Hydrogen bonding
2. Hydrophobic interactions
3. Electrostatic (ionic) interactions
4. Van der Waals interactions
5. Disulfide bridges
Why do hydrophobic interactions exist?
Hydrophobic R-groups don't interact with water molecules around them, so the water molecules become ordered around the R-groups. This is energetially unfavourable, so they clump together and move towards inside of protein to minimise exposed hydrophobic surface area.
What are Van der Waal's forces?
-Sum of attraction and repulsion forces between transient dipoles of all atoms.
- Attraction/repulsion forces are determined by distance between the atoms.
- Attraction occurs when attraction is greater than repulsion.
What is the limitation of disulfide bonds?
They are unable to form inside cells due to intracellular environment being reducing. Only occurs on extracellular proteins.
What are the relative strengths of these interactions (strongest to weakest)?
5. Van der Waal's
What is the structure of collagen?
- Left-handed helix.
- 3 residues per turn.
- Most common amino acid sequence is: Glycine-Proline-Hydroxyproline.
- 3 collagen molecules are held together in right-handed superhelix by H-bonds between Gly residues.
What is the importance of vitamin C in maintenance of collagen?
- Enzymes that convert proline to hydroxyproline requires Fe(II) to function.
- Fe(II) is kept in reduced state by vitamin C.
- Lack of vitamin C leads to less Fe(II), which leads to less enzyme activity, less synthesis and maintenance of collagen, resulting in scurvy.
What is another name of vitamin C?
What are motifs?
Common groupings of secondary structure elements found in proteins.
What are examples of common motifs?
- β-α-β motif
- α- helix hairpin
- Greek key motif
What is a domain?
Part of a protein whose structure (and often function) is independent of any other part of the protein.
What is the structure of multi-domain proteins?
Proteins are made out of multiple domains joined together by linkers.
What is the overall structure of proteins?
Protein → Subunits → Subdomains
What techniques can be used to determine protein 3D structure?
1. X-ray crystallography (electron density maps)
2. Cryoelectron microscopy
What methods can be used to purify proteins?
1. Affinity chromatography: Protein of interest bind to specific complementary proteins inside column.
2. Ion exchange chromatography: Separation based on charge. Salt of increasing concentrations added. Only the most charged proteins will remain bound for the longest time.
3. Gel filtration chromatography: Beads only permeable to certain sized proteins. Smaller proteins take longer to travel down column.
How do proteins fold?
1. The protein folds into its general shape very quickly as a result of hydrophobic interactions, in a process called hydrophobic collapse.
2. Small adjustments are driven by other forces of interactions.
3. Larger proteins need the aid of chaperones to fold.
How can misfolded proteins cause disease?
- Misfolded proteins (amyloids) form aggregates that damage tissues.
- Diseases such as Alzheimer's and Parkinson's are thought to be caused by misfolded proteins.
What structural elements of proteins relate to their function?
- 3D shape
- Hydrophobic/hydrophilic regions
- Polymer - lots of energy
What are cofactors?
Molecules used by a protein to provide chemical reactivity not found in amino acids of the protein.
What are the types of cofactors?
1. Prosthetic group: Bound tightly to the protein (e.g. haem)
2. Co-substrate: Binds loosely to the protein and is released after protein carries out its function
Why are cofactors especially needed for redox reactions?
Because no amino acids are capable of carrying electrons and oxygens.
What are co-enzymes?
Cofactors needed for enzymes to function.
What are common co-substrates coenzymes?
- NAD+/NADP+ (from niacin - B3)
- CoA ( from pantothenate - B5)
- Tetrahydrofolate (from folic acid - B9)
What are common prosthetic group coenzymes?
- FMN/FAD (from riboflavin - B2)
- Thiamine pyrophasphate (from thiamine - B1)
- Adenosylcobalamin (from cobalamin - B12)
- Methylcobalamin (from cobalamin - B12)
What is the difference between prosthetic group and co-substrate?
Prosthetic group remains attached to protein when it is regenerated whereas co-substrate detaches.
What are the differences between haemoglobin and myoglobin?
- Haemoglobin facilitates O2 transport in blood while myoglobin facilitates O2 diffusion in muscles.
- Haemoglobin is a heterotetramer of 4 subsunits while myoglobin is a monomer of 1 subunit.
- Myoglobin dissociation curve is hyperbolic while haemoglobin dissociation curve is sigmoidal. Myoglobin is not an allosteric protein.
What is responsible for the flexibility of proteins?
Ability for proteins to break and reform weak interactions between amino acids.
What is responsible for the cooperative nature of haemoglobin?
- Binding of O2 to Fe in haem causes the Fe to be pulled into the plane of the porphyrin ring.
- This causes F-helix in subunit to be pulled downwards also.
- Position of FG loop at subunit interface also changes, causing conformational change in neighbouring subunits that increase their O2 binding affinity.
- Causes conformational change in all 4 subunits that decrease diameter of central pore.
- Subunits are closely packed, reducing length of Fe-O2 bond and thus increasing affinity of Hb to O2.
What are the 2 states of haemoglobin?
- Low affinity (T) state
- High affinity (R) state
What are the 2 models for cooperativity?
What is required for the existence of transmembrane proteins?
Hydrophilic extramembranous domains and hydrophobic transmembrane domains.
What are the typical compositions of transmembrane domains?
- Rich in α-helices and β-pleated sheets as these structures are hydrophobic (due to no available atoms for hydrogen-bonding).
- Rich in hydrophobic amino acids.
What is an immunoglobin fold?
β-sandwiches made from greek key domains
What is the structure of antibodies?
- Each antibody is made from 2 identical heavy chains and light chains stabilised by disulfide bonds.
- Variable domains form the antigen binding sites.
- Constant domains of heavy chains form recognition sites for B-cells.
What is the structure of antibody heavy chains?
- Each heavy chain consists of 1 variable domain and 3 constant domains.
- Hinge region connects 1st and 2nd constant domains.
What are the different isotopes of antibodies?
1. IgM (5 per group)
2. IgD, IgE, IgG (1 per group)
3. IgA (2 per group)
What is the name given to the binding site of antibody to the antigen?
What are the 3 characteristics of enzyme-catalysed reactions?
- Greater rate of reaction
- Greater specificity (fewer by-products)
- Capacity for regulation
What mechanisms are used by enzymes to speed up rate of reaction?
- Acid/base catalysis
- Covalent catalysis
- Proximity effect
- Substrate strain
What is the importance of the 3D shape of the enzyme?
The majority of the 3D shape of the enzyme is to create/maintain the shape of the active site.
What are the properties of the active site?
1. Binds substrates selectively
2. Has correct properties to catalyse reaction
3. Releases products rapidly
What mechanisms does carbonic anhydrase use to catalyse its reaction?
- Acid/base catalysis: His 64 accepts H+ from H2O to stabilise OH-.
- Covalent catalysis: OH- binds to Zn2+ via dative covalent bond.
- Proximity effect: CO2 brought close to the OH- in active site.
- Substrate strain: H2O dissociated into H+ and OH- as a result of the active site.
Why are serine proteases named so?
They contain Ser residue in active site.
What is the catalytic triad in serine proteases?
1. Ser 195
2. His 57
3. Asp 102
What are the roles of each member of the ser protease catalytic triad?
- Ser195: Nucleophilic attack
- His57: Acid/base catalysis
- Asp102: Stabilises charge on His
How do ser proteases select for specific proteins?
- Chymotrypsin selects large hydrophobic molecules
- Trypsin selects for +ve molecules
- Elastase selects for small molecules
What mechanisms do Asp proteases use to catalyse reactions?
1. Acid-base catalysis: Asp 2 acts as base and accepts H+ from H2O.
2. Proximity effect: H2O and peptide bond both held in close proximity to each other in active site.
3. Substrate strain: O-H in Asp 1 stabilises charge on O- in tetrahedral intermediate.
How is HIV protease inhibition achieved?
- Saquinavir mimics tetrahedral transition state of HIV protease, but has non-cleavable peptide bond due to presence of tetrahedral C-H instead of trigonal plainer C=O.
- Flaps ensure the drug molecule is stuck in active site and cannot be released, inhibiting the protease.
What are the different classes of enzymes?
1. Oxidoreductase: Redox reactions
2. Transferases: Transfers groups between different molecules
3. Hydrolases: Hydrolysis reactions
4. Lysases: Breaks covalent bonds by other means (e.g. double bond/ring formation)
5. Isomerases: Alters structure but not chemical composition
6. Ligases: Join molecules together using ATP
Why are initial rates used when dealing with enzyme kinematics?
- In order to make assumption there's no E + P → ES reverse reaction since [P] is low.
- Initial rates unaffected by equilibrium.
- Initial rates unaffected by Δ[S] during reaction.
What do the terms in the Michaelis-Menten equation relate to?
- V_Max: Efficiency/turnover of enzyme.
- K_M: Affinity of enzyme for substrate, hence [S] needed for enzyme to work.
What is the significance of K_M?
- K_M is a measure of the affinity of the enzyme for the substrate.
- The lower K_M, ther higher the affinity.
What is the significance of K_CAT?
The greater the value of K_CAT, the greater the efficiency of the enzyme.
What are activators?
Molecules that promote enzyme activity.
What are inhibitors?
Molecules that inhibit enzyme activity.
What are the kinematic effects of competitive inhibitors?
Increases K_M but keeps V_Max constant
What is the theory for competitive inhibition?
- Transition state mimic binds to active site of enzyme with higher affinity than substrate.
- Competitive inhibitors of enzymes used as drugs are designed to mimic transition state.
What are non-competitive inhibitors?
- Molecules that bind to a site on the enzyme away from the active site.
- Alters the 3D shape of the enzyme and arrangement of catalytic residues to decrease the catalytic activity of the enzyme.
- Only binds to ES complex so has no effect on K_M.
What are the kinematic effects of non-competitive inhibitors?
Decreases V_Max but keeps K_M constant
What are irreversible inhibitors?
Molecules that bind to the active site and form covalent bonds with the enzyme in initial reaction (completion inhibited), permanently inhibiting the enzyme.
What enzyme does penicillin inhibit?
- Glycopeptide transpeptidase
- Crosslinks pepidoglycan chains in bacterial cell wall
- Penicillin is suicide inhibitor
How can phosphorylation be used to control enzyme activity?
- Active site: Phosphorylation of active site blocks substrate binding
- Conformational change: Phosphorylation at allosteric site causes conformational change at active site that activates/inhibits enzyme
How do zymogens control rates of reaction?
- Cleavage of a part of the enzyme causes conformational change in the active site that activates the enzyme.
- This change is irreversible.
What are the different forms of enzyme control?
2. Covalent (e.g. phosphorylation)
3. Substrate level
What is allostery?
- The ability for an enzyme to undergo conformational changes that alter its activity.
- This can be in response to substrate binding (cooperativity) or allosteric regulator.
Why does glucokinase display cooperativity?
1. Binding of glucose causes shift of glucokinase from super-open to open state. This is a slow process.
2. Binding of ATP to the open state causes transition to closed state and the reaction to takes place. This is a quick process.
3. Once the reaction has taken place, the products are released from the active site.
4. In the presence of high [glucose], glucose quickly binds to the enzyme and open state formed again. This is able to quickly take part in reactions once ATP binds.
5. In the presence of low [glucose], enzyme returns to super-open state and slow transition to open state is required again before enzyme can catalyse reaction.
What is the clinical significance of glucokinase?
- Mutations in glucokinase are associated with neonatal diabetes and MODY(Maturity Onset Diabetes of the Young).
- Artificial allosteric regulators can be used to activate glucokinase.
What is homotrophic allostery?
- Binding of substrate increases affinity of enzyme for substrate.
- Enzyme has sigmoidal kinetics curve.
What is heterotropic allostery?
- Binding of activator to allosteric site on enzyme stabilises structure of enzyme and locks it in high affinity state. Curve becomes hyperbolic.
- Binding of inhibitor disrupts the structure of enzyme and locks it in low affinity state.
What is an example of enzyme regulation by allostery?
- Cooperativity for fructose-6-phosphate
- Has allosteric site for ATP which is inhibitor
What is an example of enzyme regulation by phosphorylation?
- Glycogen phosphorylase
- Cooperative enzyme
- Allosteric inhibition by ATP and glucose-6-phosphate
- Phosphorylation by phosphorylase kinase in response to cAMP pathway