Term
| Stereoisomers of Amino Acids |
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Definition
| L (left) and D (right) forms. Humans only use L-form. Bacteria use both. |
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Term
| Hydrophobic (non-polar) Amino Acids |
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Definition
Alanine (Ala, A)
Valine (Val, V)
Proline (Pro, P)
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
Leucine (Leu, L)
Isoleucine (Ile, I)
Methionine (Met, M): Start codon |
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Term
| Hydrophilic (polar) Amino Acids |
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Definition
Can form H/Covalent bonds.
Glycine (Gly, G): Non-chiral (H for R-group)
Serine (Ser, S)
Cysteine (Cys, C): Contains S, can form disulfide bonds (then called cystine).
Asparagine (Asn, N)
Threonine (Thr, T)
Histidine (His, H)
Glutamine (Gln, Q)
Tyrosine (Tyr, Y) |
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Term
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Definition
At pH7.
Aspartate (Asp, D) and Glutamate (Glu, E) have negatively charged R-groups.
Lysine (Lys, K) and Arginine (Arg, R) have positively charged R-groups. |
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Term
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Definition
At pH0, animo acid is ionized (NH3+ and COOH)
At pH7, hydroxyl group is ionized (NH3+ and COO-)
At pH14, amino group loses proton (NH2 and COO-) |
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Term
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Definition
| pH were 50% of the sample becomes ionized (between COOH and COO-). COOH always ionizes before NH3+. |
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Term
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Definition
| Dehydration/condensation reaction links amino acids in peptide bond. Bond between Carboxyl and amino group. |
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Term
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Definition
| Chain of Amino Acids. Since the amimo and carboxyl groups are linked, only the N (amino) and C (carboxyl) terminus will ionize. Thus, ionization of R-groups affects folding (rather than ionization of carboxyl and amino groups). |
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Term
| Ion Exchange Chromatography |
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Definition
| Manipulate the pH so that protein you want sticks to a charged lattice (protein has the opposite charge of the lattice) while all the other proteins pass through. Then, change the pH so that you can collect the desired protein. |
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Term
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Definition
| pH at which the protein has a net charge of 0. |
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Term
| Partial Double bond Nature of Peptide Bonds |
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Definition
| Double bond can go from O/C to C/N. Lack of free rotation restricts folding ability and keeps everything in the same plane. Stearic interference can restrict rotation. |
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Term
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Definition
α-helix: 3-4Å across. Formed via H-bonds between an amino H atom and a Carbonyl H atom four amino acids down the chain. Pitch = 5.4Å. Folding ensures lowest interference and max H bonds. 30% of amino acids.
β-sheet (pleated sheet): H bonds between different sections of the same chain or different chains. Parallel = chains running in same direction. Antiparallel = chains running in opposite directions. 20-25% of amino acids.
Loops and Turns: Flexible region that allows chain to significantly change direction. Usually consist of glycine and proline (reduces interference). 45-50% of amino acids. |
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Term
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Definition
| Final 3-D shape of a single polypeptide chain. Either fibrous (elongate, structural) or globular (have chemical function). |
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Term
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Definition
| Globular proteins can fold into 2 or more regions (domains) that each have a specific function. |
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Term
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Definition
Hydrophobic interactions: 1st mechanism that generates folding. Prevent unfolding. Follow hydrophobicity index (the most hydrophobic molecules end up in centre of protein).
Hydrogen Bonds: Max number form in folded protein.
Ionic Bonds: Mostly form on surface of protein.
Disulphide Bonds: Form between cysteine (linked cysteine called cystine). Don't play a role in shape. Used to hold two polypeptide chains together (important in 4° structure).
Metal Ions (Zinc Fingers): A location were zinc is found. Used to stabilize. |
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Term
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Definition
| Two or more polypeptide chains. 2 = dimer, 3 = trimer, 4 = tetramer. 2 of the same polypeptide = homodimer. 2 different polypeptides = heterodimer. |
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Term
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Definition
Tetramer with 2 αβ heterodimers. Can potentially carry 4 oxygen molecules.
T-state = normal state, will not bind O2 (deoxyhaemoglobin).
R-state = picks up O2 (oxyhaemoglobin).
Allosteric: O2 binding to one subunit causes next subunit to pick up O2. |
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Term
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Definition
| Oxygen carrying protein in muscle. Contains the prosthetic group protoporphyrin that has a tertapyrrhole shape. Protoporphyrin has central Fe2+ that is linked to 4 nitrogens. |
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Term
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Definition
| Non protein group that is essential to protein function. |
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Term
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Definition
| Process involves ferrocheletase (adds ferrous ion) and ALA dehydratase. Lead poisoning inhibits both ferrocheletase and ALA dehydratase resulting in accumulation of ALA and deficiency of Haem. Lack of Haem results in anaemia and decrease in energy generation. Accumulation of ALA thought to be the cause of characteristic nuerological symptoms. |
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Term
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Definition
| α-helix. On the eighth amino acid from the N-terminal is a histadine. The Fe2+ of the protoporphyrin links to this histadine. The Fe2+ can potentially oxidize to Fe3+ in the presence of oxygen (Fe3+ cannot bind oxygen). Thus, the globin portion of the protein stops this from happening. |
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Term
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Definition
| The partial pressure of O2 that results in 50% saturation of protein. P50 Myoglobin = 2.8torr (very efficient). As pO2 is lowered, myoglobin released O2 (maintains O2 equilibrium in cell). |
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Term
| Myoglobin vs. α and β Globin |
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Definition
| Myoglobin has virtually the same shape as α and β globin. However, there primary structures have less than 20% of the same amino acids (due to invariant amino acids). |
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Term
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Definition
| Amino acids that are essential for folding a protein into its final shape. |
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Term
| Conservatively Substituted Amino Acids |
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Definition
| Amino acids that can be substituted for another amino acids with the same chemical properties (without affecting protein shape). |
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Term
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Definition
| Myoglobin was first. Other globins branched off. |
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Term
| O2 Dissociation curve of Haemoglobin |
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Definition
| Has a sigmuidal shape (showing co-operativity). P50 of 28torr (higher than myoglobin). |
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Term
| Oxygen Binding to Haemoglobin |
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Definition
| When O2 binds to the ferrous ion in the prosthetic group it pulls it down (making it level with the nitrogens on either side). This in turn pulls down the histine, which in turn pulls the F-helix, changing the proteins shape. This shape change causes the affinity of the next subunit to increase. |
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Term
| 2,3 Bisphosphoglycerate (BPG) |
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Definition
| BPG is found in red blood cells in equal concentration to haemoglobin (4.5nM). BPG has three negative groups which ionically bind with the positive charges at the centre of haemoglobin, causing haemoglobin to go into its T-state. In the lungs, 100 torr partial pressure forces the BPG out of the haemoglobin, causing the haemoglobin to enter R-state. In the tissues, 25-30 torr partial pressure is low enough that the O2 is released and replaced by BPG (again causing T-state). Lower O2 affinity of Haemoglobin is due to BPG. BPG causes shift to right in oxygen affinity graph. |
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Term
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Definition
| CO2 and water in blood is converted to carbonic acid by Carbonic anhydrase. The carbonic acid then dissociates into protons and bicarbonate. The protons bind to haemoglobin forcing it towards its T-state, and causing it to release O2. Thus, CO2 in theblood causes O2 release. |
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Term
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Definition
| Has gamma globins rather than beta globins. Gamma globins have serine rather than histadine at position 143. This reduces the amount of positive charges, thus reducing BPG's ability to bind. Less oxygen is required to move foetal haemoglobin into R-state (giving it a greater O2 affinity than adult haemoglobin). Allows both maternal and foetal tissues to recieve oxygen. |
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Term
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Definition
| Caused by A to T mutation in beta globin gene. Causes hydrophobic valine outdent that can bind to the hydrophobic cleft that is present in normal haemoglobin. Binding of haemoglobin causes them to form chains, changing the shape of the red blood cell. Sickle cells can block capillaries due to there rigid shape and increased stickiness. Sickle cell causes lower risk of malaria. |
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