Proteins

Question	Answer
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

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	Created by Ifeoma Ezepue about 9 years ago