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ProteinStructure/Fun

Biochemistry, Medicine, Phase 1

TermDefinition
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