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ProteinStructure/Fun
Biochemistry, Medicine, Phase 1
| Term | Definition |
|---|---|
| Proteins | primary sequence of amino acids encoded by DNA; define structure and function of proteins |
| Globular and fibrillar proteins | types of proteins |
| Collagen, keratin | structural proteins |
| Typsin, DNA polymerase | movement proteins |
| Haemoglobin, transferrin | transport proteins |
| sodium/potassium ion pump | membrane transport proteins |
| insulin | hormone protein |
| acetyl choline receptor | receptor protein |
| antibodies, clotting factors | defence proteins |
| histones | gene regulation proteins |
| tubulin | chromosome sorting protein |
| Peptide bond | has some features of a 'double bond', shorter than expected C-N bond length rigid C-N bond, no rotation, trans arrangement of groups; partial positive charge on O atom of carboxyl terminus and light negative change on N atom of amino terminus |
| H-bonds | peptides can form H-bonds with other polar groups (including peptide bonds) in polypeptide chain (e.g. alpha helix) |
| Direction of polypeptides | first aa NH3+ group (N-terminus) last aa has COO- group (C terminus) |
| Disulphide (S-S) bridges | covalent bond between two cys joining the subunits together, e.g. insulin |
| Polypeptides and proteins | Not branched like sugars; peptides are the main covalent bond |
| Glycosylation | other covalent linkages; the reaction in which a carbohydrate is attached to a hydroxyl or other functional group of another molecule; O-lniked-OH of thr and ser; N-linked -NH2 of asn |
| Phosphorylation | another type of covalent linkage; post-translational modification; cell signal transduction, e.g. phosphorylation of try in insulin receptor; change in activity of enzyme, e.g. phosphorylation of glycogen phosphorylase in response to glucagon |
| Methylation | type of covalent linkage; post-translational modification; via -NH2 groups of lys and arg ; e.g. histones affecting gene expression |
| Phosphotate | large negatively charged process; adding it to a protein will then largely change the function of a protein due to its size and large charge |
| 10 - approx. 3600 aa | size range of proteins |
| Dipeptides | a few naturally occurring examples; made up of only two amino acids |
| Aspartame | asp-phe; artificial sweetner; example of a dipeptide |
| Tripeptides | glutathione (glu-cys-gly); natural antioxidant |
| Short peptides | 10-40 aa; peptide hormones (glucagon; 29aa); neurotransmitters (Substance P, 10aa) |
| Large polypeptides | proteins; >40aa |
| Large proteins | dystrophine (3684aa) |
| 4 levels of 3D structure of proteins | primary, secondary, tertiary, quaternary |
| Primary level | sequence of amino acids in a peptide chain |
| Secondary level | folding/coiling of peptide chain (usually into an alpha-helix or beta-pleated sheet) |
| Tertiary level | peptide chain folds upon itself |
| Quaternary level | folded peptide chains join together |
| alpha-helix (1) | type of folding/coiling of a peptide chain; secondary level structure of proteins; amino acid side chains stick outwards; arrangement due to the strength of the hydrogen bonds; allows for best stabilisation energy between H bonds; |
| alpha-helix (2) | formed by H-bonds in the same polypeptide chain (backbone NOT side chains); regular right-handed helix; 3.6 residues/turn stabilised by H-bonds; rigid cylinder shape serves as architectural support for protein |
| H-bonds of the alpha helix | formed between peptide bond carbonyl-O and H of N-H every 4th peptide |
| distance between troughs of alpha helix | 0.54 nm |
| beta sheet distance between troughs | 0.7 nm |
| beta-sheet | linear peptide chains; hydrogen bonding between peptide chains holds strands together in beta sheet; side chains in each strand alternately lie above and below the plane of the sheet |
| types of beta-sheet structures | (A) antiparallel with a beta-hairpin bend; widespread in globular proteins (B) parallel with upper curve toward C terminus and lower curve toward N terminus |
| collagen triple helix | three chains; found in collagen; H-bonds between (not within) chains; 3 resides/turns; left-handed helix |
| amino acids of collagen triple helix | gly - x - y- gly - x - y; x = mainly proline; y = mainly hydroxy-proline |
| proline | cannot go into alpha helix |
| Glycine | does not have an R group which may explain why it is used; results in a more compact structure |
| proteins and secondary structure | different proteins combine different amounts of alpha helices and beta sheets |
| Haemoglobin secondary structure | 60% alpha-helix; actin molecule as positive end; |
| proteins with high % of beta sheets | fibrillar proteins (silk fibres aka fibroin); properties of high tensile strength but no elasticity |
| supersecondary structure | combinations of alpha-helix and beta-sheet form common domains found in proteins; 100s exist; quite common; certain arrangements frequently found because they are the most energetically stable; the low range suggests this stability |
| beta-barrel, beta-sandwhich, Rossman fold | examples of domains; unclear what the functionality is |
| tertiary structure | how the whole polypeptide (subunit) is folded in 3D; will consist of a number of different supersecondary structures (domains) |
| quaternary structure | how the whole functional protein is formed in 3D; may consist of a number of subunits e.g. haemoglobin alpha2beta2 |
| covalent forces that stabilise protein structure | disulphide bridges (not all proteins have them) |
| non-covalent forces that stabilise protein structure | hydrogen bonds, electrostatic interactions, Van der Waals forces, hydrophobic effect |
| Types of hydrogen bonds in proteins | 2 electro negative atoms compete for the same atom; H-Bond donors; H-bond acceptors |
| H-bond donors | positively charged side chains; Trp, His, Arg, Lys |
| H-bond acceptors | negatively charged side chains; Trp, His |
| Hydrogen bond requirements | need to be close enough for optimal strength; 0.28 nm optimal length; the energy required is not a great deal (per bond), requires low entropy |
| Electrostatic interactions | between charged side chains, at physiological pH (7); Asp and Glu carboxyl groups are ionised and Gln and Asn amino groups are ionised |
| Van der Waals forces | is the sum of the attractive or repulsive forces between molecules; excluding those to covalent, hydrogen and electrostatic bonds; dependent on dipole affect caused by the unequal distribution of electrons |
| Partial dipoles (1) | partial negative dipole and partially positive charge dipole charge across a covalent bond; nuclei of the hydrogen atoms naturally repel when close together because they are both positively charged; |
| Partial dipoles (2) | at a certain distance away from each other there is a slight dipole attraction that strengthens the bond that requires very low energy |
| Hydrophobic regions | fold in such a way that to minimise contact with an aqueous environment; they are unable to form hydrogen bonds |
| Stabilisation energy in a protein | quite small but very sensitive to denaturation |
| Denaturation | caused by to high or lo pH; temperature, ionic strength of a solution |
| Protein folding pathway | the thousands of possible structures a protein can fold; only one of which is functional; the amino acid sequence that encodes the final structure but also the pathway that leads to that structure |
| Misfolded protein diseases | sickle cell disease; Alzheimer's disease; Creutzfeldt-Jakob disease |
| Sickle cell disease | Glu > Val subsitution; Val is charged to hydrophobic; the result of the misfold is an abnormal haemoglobin (HbS); the switch from Glu to Val causes the cell to want to stabilise (protect the hydrophobic regions) resulting polymerisation |
| Alzheimer's disease and CJ disease | diseases that result from the formation of stable aggregations of proteins; amyloid proteins forming in plaques; prion protein polymerisation in CJ disease |
| Polymerised sickle-cell haemoglobin (Hbs) molecule | crystallised chain structures which disrupt the membrane of red blood cells |
| Creutzfeldt-Jakob Disease (CJD) neurological symptoms | difficulties with walking, slurred speech, numbness, dizziness, visual problems |
| Creutzfeldt-Jakob Disease (CJD) psychological symptoms | severe depression, withdrawal, anxiety, irritability, insomnia |
| Creutzfeldt-Jakob Disease (CJD) prion protein | PrP conversion from the normal, cellular form PrPC to that pathogenic form PrSC |
| Polymerisation of the pathogenic form (PrPSC) | forms fibrils (aggregates) |
| Normal prion protein | PrPC, alpha helical, susceptible to proteolysis |
| Mutant prion pro | PrPSC, beta sheet becomes present, protease resistant so it accumulates; identical amino-acid sequence to normal prion protein |
| prion | a protein that can fold in multiple, structurally distinct ways, at least one of which is transmissible to other prion proteins; found on the surface of cells |
| Non-coded amino acids | those not naturally encoded or found in the genetic code of any organisms |
| Hydroxproline | non-coded amino acid; hydroxylation of proline; important component of collagen; allows for specific triple helix structure |
| Selencysteine | non-coded amino acid; encoded by subset of STOP codons, contains Se instead of S; reduced pKa useful for enzymes in anti-oxidant activity |
| Homocysteine | non-coded amino acid; extrra methyl group compared to cysteine; needed to synthesise cysteine; not found in proteins |
Created by:
emmaallde
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