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Proteins 1
Biochem and medical genetics
| Question | Answer |
|---|---|
| Three main molecules in the body | Lipids, Proteins, Carbohydrates |
| Main inorganic molecules in the body | Water/Oxygen, Minerals, Ions |
| Key organic molecules in the body | Vitamins Hormones Pigments |
| Size of proteins/cells and how to view | Proteins- 2-20 nm view with X-ray crystallography and cryo-electron microscopy Cells- 1-100 um view with light or scanning electron microscopes |
| Why understand molecular basis | Facilitates drug discovery and intervention cancer diabetes developmental disorders asthma hypertension |
| What are Macromolecules | Synthesised in the cell from small monomers obtained in our diet e.g. proteins from amino acids (which occurs in ribosomes due to low water environment) |
| What types of bond form in macromolecules | Amino acids form peptide bonds Fatty acids and glycerol for ester bonds Sugars form glycosidic bonds |
| Describe basic protein structure | Amino acids covalently bond Primary structure in peptide chain Repetitive H bonds give secondary structure of regular elements These pack together to give a tertiary structure The quaternary structure is the interaction of multiple polypeptides |
| Describe how amino acids exist | At pH 6 amino acids have no charge (Coo- and NH3+) These are zwitterions There are 20 main amino acids They are non -polar, charged polar or uncharged polar |
| 4 main categories of amino acids | Positively charged Negatively charged Uncharged polar Hydrophobic Special cases |
| Describe chirality of amino acids | The alpha carbon have 4 different groups attached so is a chiral centre Two different enantiomers exist in either L or D form All amino acids in proteins are L form |
| Why is Ornithine different? | Is not coded for by DNA- is non-proteinogenic Plays a central role in urea cycle Abnormally accumulated in ornithine transcarbamlyase deficiency |
| Why is GABA different | Major inhibitory neurotransmitter that binds to a GABA receptor to dampen resting potential The amino group is bound to the gamma carbon, not alpha |
| Explain post translational modification to Hydroxyproline | A hydroxyl group is added to proline by prolyl hydroxylase to the gamma carbon. This required vitamin C, so scurvy shows low Hpy and weak collagen Allows for tight, stable binding of collagen helix due to H bonds Increase levels seen in Paget's disease |
| Explain post translational modification to Hydroxylysine | Synthesised from lysine via oxidation on the 5th carbon by lysyl hydroxylase. Provides a like for sugars allowing for cross linking of collage and ensuring stability. Ehlers Danols syndrom is due to mutations in the enzyme needed for this. |
| Examples of post translational modifications | Glycosylation Phosphorylation- serines, theronines and tyrosines Hydroxylation- to proline and lysine Ubiquitination- addition of ubiquin proteins to lysine via ubiquitin ligases Sumolyation- addition of SUMO groups via sumo ligases Acetylation |
| Addition of lipid to amino acids | Farsenyl and Geranyl pyrophosphate are lipid molecules known as isoprenoids. These attach to proteins by farnesyl transferase to cystine at CAAX motifs This has several roles including anchoring proteins to membranes due to their hydrophobic nature |
| Gycosylation | Covalent attachment of oligosaccharides to protein side chains. Glycoproteins appear mainly on secreted or cell surface membranes. They can alter structure/function, target a certain protein, give a cell identity or protect a cell |
| Types of Glycosylation | N-glycosylation O-glycosylation Glypiation (to lipids) C-glycosylation Phosphoglycosylation These can help ensure proteins fold properly and any not folded are destroyed or refolded |
| Properties of the Peptide bond | A resonance structure, electrons are shared along the CO-NH system so partial charges appear on O and N. This means it shows double bond characteristics. It is a rigid, planar structure due to no rotation around the bond and has angles of phi and psi. |
| Motifs of Protein Structure | Alpha structures Alpha-beta structures Beta structures These for simple motifs, which connect to form functional domains which are the fundamental unit of tertiary structure. This is a stable unit |
| Forces holding atoms and molecules together | Covalent bonds Hydrogen Bonds Ionic interactions Van de Walls interactions Hydrophobic effect |
| Van de Waals forces | Exist as weak repulsive or attractive forces which arrise from fluctuations in electron charge densities of neighbouring atoms These are weak but their sum is significant Repulsive forces result from close approach of electron density clouds. |
| Explain the Alpha helix | Stretches of amino acids with phi and psi angles of -60 and -50. 3.6 residues a turn with h bonds between the C=O of residue n and the NH of residue n+4. Other variations exist, such as n+3 and n+5, but these are less stable Found in membrane proteins |
| Properties of alpha helix | Always right handed except in a few cases R groups project outwards so do not effect the helix There is a dipole from C to N terminus, which is amplified by the hydrophobic interior of a cell membrane Proline has a cyclical structure so breaks the helix |
| Beta Sheet | Stronger than Alpha helix due to hydrogen bonding present. Parallel sheets are strongest as h bonds are parallel Antiparallel have diagonal h bonds Can also get mixes f parallel and antiparallel sheets |
| Loop Regions | Many protein secondary structures are made of alpha helixes and beta sheets joined by loop regions. Loop regions are at the surface with main chain CO and NH exposed to form h bonds. These contain charged, polar hydrophilic residues for binding sites. |
| Types of loop region | Hairpin loops- connect two adjacent antiparallel bate strands Reverse turns are short hairpin loops with two types: Oxygen double bonded to carbon facing inwards or outwards. |
| Simple Motifs | Secondary structural elements combine to form simple motifs. These are not independent but are combinations of other elements. These make up the tertiary structure. The helix turn helix motif in DNA and Calcium binding proteins is one example |
| Calmodium simple motifs | Calmodium is a key component of calcium signalling pathways. This is mad up of 4 EF hands. This binds to 4 Ca2+ ions and changes shape to facilitate interaction and activation of kinases and to initiate intracellular signals |
| List some common motifs | Hairpin Beta Motif- two adjacent antiparallel beta strands joined by a loop Greek key motif- Four adjacent antiparallel beta strands The b-a-b motif- a common way to connect parallel beta strands |
| What is structural Homology | When two domains in different polypeptide chains have a significant similarity in their amino acid sequence |
| What are domains? | These are made of combinations of secondary structure and motifs. Motifs appear structurally stable and need the same amino acids to form, so similar domain structures occur in different proteins with different functions and amino acid sequence, |
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