|What are some roles of proteins?
|structural catalysts (enzymes) carrier (haemoglobin) protective (antibodies) signalling (receptors)
|What is the function of a protein determined by?
|external chemistry and shape ^determined by amino acid composition diff AA have diff chemical and structural properties
|What are the levels of protein structure?
|primary - sequence of AA secondary- 2D fold tertiary- 3D fold quaternary - interaction of subunits
|What are two key features of the primary structure of a protein?
|N-terminus -amino terminus (H3N+) C-terminus -carboxyl terminus (COO-)
|How many different R groups are there? Why are they important?
|20 result in a variety of chemical properties: hydrophobic/hydrophilic polar/non-polar structural
|Which amino acids have nonpolar, aliphatic side groups?
|glycine, Gly G alanine, Ala A valine, Val V leucine, Leu L methionine, Met M isoleucine, Ile I
|Which amino acids have aromatic side groups?
|Phenylalanine, Phe F Tyrosine, Tyr Y Tryptophan, Trp W
|Which amino acids have positively charged side groups?
|Lysine, Lys K Histidine, His H Asparagine, Asn N
|Which amino acids have negatively charged side groups?
|Glutamate, Glu E Aspartate, Asp D
|Which amino acids have polar, uncharged side groups?
|Serine, Ser S Threonine, Thr T Cysteine, Cys C Proline, Pro P Aspartate, Asp D Glutamine, Glu Q
|What is the peptide bond?
|bond that holds adjacent AA together structural implications: planar, H bonding
|What differentiates a protein from a peptide?
|chains from 50+ are classed as proteins
|Why is there such a huge variation in proteins?
|50-2500 AA in a typical protein 20 possible AA per positon so huge variation
|What is the secondary structure of a protein determined by? What are the two main types?
|the interactions between the peptide bonds via hydrogen bonding two main types: a-helix and B-sheet
|Explain the a-helix secondary structure
|3.6 residues per 360degturn stabilised by H bonding between peptide bonds - results in 0.54nm pitch R groups point downwards
|Explain the b-sheet secondary structure
|forms a flat sheet surface with strands of protein alongside stabilised by H bonds between amide links strands can be parallel or anti-parallel b-sheets can be stacked to form 3D structure
|What is the tertiary structure?
|the 3D fold of the protein which brings together secondary structure in 3D space
|What is the quaternary structure?
|a fold of 3D folded not all proteins have quaternary structure can be homo or hetero e.g. haemoglobin (4 subunits)
|Explain the structure of collagen
|strong 3D structure triple helix with a large number of prolines in a Pro-Pro-Gly staggering of the three chains helps H-bonding btw chains
|What is the result of post translational modification of amino acid side chains?
|covalent strand crosslinks includes di-sulphide bonds between cysteine and lysine
|What is the nomenculture of proteins based on?
|3D shape globular -majority of proteins -overall globular shape, with a mix of 2nd structures fibrous -extensive packaging of 2nd structure -often dominated by one type of 2nd structure -form structural proteins e.g. collagen, keratin
|Proteins can be made up of domains. What are protein domains?
|discrete regions of 3D structure
|What are proteins produced by?
|ribosomes (translation of RNA to proteins)
|What is the hydrophobic effect?
|the observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules in proteins this means you get a hydrophobic centre the exceptions to this is membrane proteins
|What are molecular chaperons?
|a diverse group of proteins that assist with the folding and in some cases unfolding of proteins but are not involved in the usual biological functions for these proteins
|When do levels of chaperones increase?
|when the cell is subjected to stress e.g. heat shock
|How do chaperones help with folding?
|some bind to hydrophobic residues and prevent hydrophobic effect driven folding e.g. HSP70 some act to protect the folding protein from the cytoplasm e.g GroEL chaperones often use ATP to provide energy to the folding process
|What are some causes of protein folding diseases?
|inherited mutation environmental stress mechanism -loss of function -toxic gain of function -dominant negative
|What are some diseases associated with protein folding?
|neurodegeneration -Alzheimer's -Parkinson's metabolic disorders -monogenic obesity cancer
|What are the four types of post translational modification of proteins?
|addition of other functional groups -acetate, phosphate, lipids addition of other proteins/peptides -Ubiquitination changing the chemical nature of AA -Deamination structural changes -Di-sulphide, cleavage
|Explain how protein phosphorylation works
|addition of covalently bonded phosphate group by protein kinases usually Ser, Thr, Tyr alters structural conformations of a protein causing it to become activated, deactivated or changes its function (dephosphorylation done by phosphatase)
|Explain the importance of the formation of di-sulphide bonds - a post translational modification
|covalent links between cysteine residues stabilises 3D structure require specific environment to form (often found extracellularly)
|Explain the importance of cleavage
|breaks down proteins into smaller peptides and amino acids so can be absorbed and used by an organism e.g. preproinsulin --> proinsulin --> insulin
|Explain the process of Ubiquitination
|free Ubiquitin = Ub Ub activated by E1 which uses ATP to form complex with Ub E1-Ub transferred to E2 E2 joins to E3 - allows polymerization of 1 or more Ub molecules on target proteins mono-Ubation= regulatory processes e.g. endocytosis, DNA repair, transcriptional regulation multi-Ubation - labels substrate for degradation by the proteasome
|What is deamination?
|unavoidable chemical reaction in physiological conditions but can be reduced by removing reactive species from the cytosol results in structural changes - therefore, protein damage