437404
Description
Flashcards by Joanna Elliott, updated more than 1 year ago
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Created by Joanna Elliott
over 12 years ago
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| Question | Answer |
| Def. Conjugated | Contains a prosthetic group eh Haemoglobin contains haem |
| Fibrous proteins | 1. Polypeptides arranged in long strands/sheets. 2. Water insoluble. 3. Strong but flexible. 4. Structural role eg keratin/collagen |
| Globular proteins | 1. Polypeptide chains folded into spherical/globular form. 2. Water soluble. 3.Diverse functions eg enzymes, carriers etc |
| Membrane Proteins | 1. Polypeptide spans membrane either partially/completely. 2. Portion inside the membrane is water insoluble. 3. Diverse function eg receptors, ion channels, toxins |
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Image:
rama.gif (image/gif)
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1.Ramachandran plot. 2.Describes acceptable psi/phi angles . 3.Helps determine what types of Secondary structures are present. |
| Which configuration of beta sheets is more stable | Anti-parallel |
| What does a beta turn allow | Allows the peptide chain to reverse direction |
| What is a motif, + example | Supersecondary structure. Eg beta sheet-loop-helix |
| When separate motifs combine, what do they form | Domains |
| What are domains | 1. Independent folding units in the tertiary structure of proteins. 2. Individual domains have specific functions. |
| What is the driving force in the folding of domains | Hydrophobic interactions |
| What do members of the same protein family have in common | They share common domain structures |
| What 2 methods can be used to tell if 2 proteins are similar | 1. Amino acid sequence (domains have similar aa sequences). 2. Structural similarity. |
| In quaternary structures are subunits held together by covalent or non covalent interactions | Non-covalent |
| In quaternary structures what are the active sites made up of | AA residues from different subunits |
| Homomultimers | Proteins with more than one symmetry axis |
| What does Levinthal's paradox prove | That proteins know which conformation the are folding into, and that the process is not entirely random |
| Are globular proteins static? What do they do | No, they 'breathe' between different conformations |
| What do proteins fold towards | The lowest energy conformation |
| Pathway of protein folding | 1. Nucleation - rapid & reversible formation of local secondary structures form. 2. Formation of domains through aggregation of local secondary structures. 3. Domain conformations adjust to form native protein |
| PDB | Protein data bank |
| What makes up a subunit | Domain + domain |
| RMSD | Root mean square deviation. Can be used to determine the structural similarity of proteins. |
| Are domains continuous structures | They don't have to be |
| Domain classification: CATH | 1. Class (What is the major secondary structure). 2. Architecture (Describes the shape of the fold). 3. Topology (Describes the connectivity of the fold). 4. Homology (Are they evolutionary related.) |
| Orthologs | 1. Proetins that have a common ancestor due to speciation. 2. Different species. 3. Same or highly similar function. |
| Paralogs | 1. Common ancestor die to gene duplication. 2. Same or different species. 3. Different but related function. |
| Which conditions (at least 2/3) should be met when identifying homologs | 1. Significant structural similarity. 2. Significant sequence similarity. 3. Functional similarity. |
| Difference between analogs and homologs | Homologs evolved from a common ancestor whereas analogs did not. |
| NAD | 1. Found in all living cells. 2. Consists of 2 nucleotides joined together by their phsophate group. 3. A cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction |
| Rossman Fold | NAD binding domain. |
| L-Lactate dehydrogenase | 1. Metabolic enzyme which catalyses the conversion of L-lactate into pyruvate (the last step on anaerobic glycolysis). 2. The N-terminal is a Rossman fold. 3. The C-terminal is the catalytic domain and is specific to lactate/malate dehydrogenases |
| Malate dehydrogenase | 1. Catalyses conversion of malate -> Oxaloacetate. 2. N-terminal is a Rossman fold. 3. C-terminal is catalytic domain |
| Are malate & lactate dehydrogenases paralogs or othologs | Paralogs (So have a common ancestor due to a gene duplication event) |
| Which is more conserved, strucutre or amino acid sequence | Structure |
| Alcohol dehydrogenase | Catalyses the oxidation of ethanol ->acetlyaldehyde |
| Sequence diversity: Conservation of residues | 1. Core residues are more highly conserved as they are critical for protein folding and stability. 2. Functional residues are also highly conserve. 3. Surface residues have the least evolutionary constraints, and can accommodate small insertions/deletions |
| Structural diversity | 1. Core highly conserved. 2. Residue insertions usually occur in the loops connecting secondary structures. 3. Residue substitutions can cause shifts in the orientations of secondary structure |
| Functional diversity | 1. Dependent on fold. 2. 1 amino acid change can change function of a protein. 3. Proteins can share less than 10% sequence identity but have identical functions in different organisms |
| How do genomes evolve | 1. Mutational events (single base changes). 2. Insertions/deletions. 3. Duplication events. 4. New genes from other species. 5. Rearrangement of existing genes. |
| Haemoglobin: Subunits, Heme | 1. In red blood cells. 2. Has 2 a-subunits and 2 b-subunits. 3. 1 heme group per subunit (contains fe and 02) |
| Sickle cell anaemia | 1. Recessive. 2. Defective haemoglobin. 3. Glutamate (negative charge) is replaced by valine (no charge). 4. Absence of polar amino acid at that position results in aggregation of haemoglobin, which distorts the shape of red blood cells |
| What can gene duplication involve and what does it cause | 1. A signle gene. 2. A single domain. 3. Most of a chromosome. 4. A gene is copied and the second copy acquires a new function due to a mutation that the first gene doesn't get |
| What can make multi-domain proteins | 1. Gene fusion. 2. Gene loss. 3. Rearrangement of existing genes |
| What does phosphorylation do to a protein | Changes its behaviour by altering its conformation eg phosphorylation of serine 14 on glycogen phosphorylase switches it from low to high activity |
| SH3 domains | Bind to proline rich peptides |
| PH domains | These domains recruit proteins to the membrane and bind to lipids within the membrane |
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