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4 types of post-translational processing event
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The __ dictates the type of folding of a newly translated polypeptide
sequence of amino acids
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Addition of a denaturant to a protein will cause __. Removal of the denaturant will cause __
- loss of 3D structure → loss of function (& increased viscosity);
- the protein to refold spontaneously → regain of function
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The __ are the most stable form of protein folding.
native structure of proteins
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Only __ can fold correctly on their own.
smaller proteins with less complex structures
- (Protein aggregates and misfolding can happen to more complex structures.)
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In the case of more complex proteins, __ are needed.
folding chaperons
- unfold the mis-folded proteins and allow them to try again for correct folding
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Correct formation of __ bonds is important in the folding and function of proteins
disulfide
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Folding chaperones bind to __ regions in unfolded polypeptides, including those that are still being translated.
hydrophobic
(They hold the protein in an open conformation to aid its correct folding later when the polypeptide is fully synthesized.)
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processing of proteins by proteolytic cleavage
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end processing (of proteolytic cleavage)
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post-translational chemical modification: O and N glycosylations
happen in endoplasmic reticulum → only ectoplasmic domain of proteins and secreted proteins have these glycosylations.
- Chains of sugars are attached to amine group of asparagines side chain (N-linked) or hydroxyl side chain of threonine (O-linked)
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Proteins can be phosphorylated at their __ residues. Phosphorylation often affects the __ of proteins. In prokaryotes, phosphorylation is mostly seen on __ residues.
- tyrosine or serine or threonine;
- conformation & activity;
- histidine
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inteins
internal segments of proteins that are removed soon after translation.
- (The 2 external segments, or exteins, become linked together.)
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The first amino acid of the downstream __ is __. A few other amino acids within the __ sequence are also conserved. These conserved amino acids are involved in __
- extein;
- cysteine, serine, threonine;
- intein;
- the splicing process, which is self-catalyzed by the intein itself
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conformational changes
- dynamic changes within 3D structure of proteins
- non-random movements triggered by various events (e.g. binding to other molecules such as a substrate, interaction with other proteins, chemical modifications, changes in the environment, etc)
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In eukaryotes, most protein breakdown involves __
ubiquitin and the proteasome
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Ubiquitin is involved in __
- energy-dependent proteolysis reactions
- There are enzymes that attach ubiquitin molecules, single or in chains, to lysine amino acids in other proteins that are targeted for breakdown.
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Ubiquitination of a protein depends on the presence or absence of __
amino acid motifs that act as degredation-susceptibility signals and the speciic enzymes doing ubiquitination
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A protein must be __ before in can enter the proteasome. After entering the proteasome, __
- unfolded;
- the ubiquitinated proteins are degraded in it
- This unfolding probably occurs through an energy-dependent process
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Part of the protein penetrates into the major and minor grooves of the DNA in order to __
recognize and achieve direct readout of the sequence (sequence specific binding proteins)
This is usually accompanied by more general interactions with the surface of the DNA molecule, which may simply stabilize the DNA-protein complex.
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examples of specific DNA-binding motifs
- helix–turn–helix (HTH) motif
- zinc finger motif
- Leucine zippers
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The contacts formed between DNA and its binding proteins are __
non-covalent
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DNA binding proteins interact with the chemical elements in the __
major groove (sometimes also minor groove)
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To maximize contacts and specificity, many DNA-binding proteins are __
dimers
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helix-turn-helix motif
- Two α-helices separated by a turn (known as β-turn)
- The second α-helix (recognition helix) is on the surface of the protein in an orientation that enables it to fit inside the major groove of a DNA molecule (e.g. lactose repressor).
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For contact between DNA and proteins, the __ should be complementary to the chemical elements of base pairs.
- shape
- polarity
- hydrogen donor and acceptor properties of the R groups of the amino acids of the protein
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In the case of __ base pairs, hydrophobic interactions are also important.
A:T and T:A
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On the surface of the DNA helix there are __ interactions between __
- electrostatic;
- negative charges on the phosphate and positive charges on the R groups of amino acids such as lysine and arginine
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In an helix-turn-helix motif with DNA, __ are made between one α-helix and the DNA backbone and also bonds formed between the __
- hydrogen bonds & salt bridges;
- recognition α-helix & major groove of DNA chemical elements
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examples of the R chains of amino acids interacting with major groove chemical elements
- T:A and C:G
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Cys2His2 finger
- a type of zinc finger protein: The zinc atom is held between 2 cysteines within the β-sheet of the motif and 2 histidines in the α-helix
- The a-helix is the part of the motif that
- makes contacts within the major groove.
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Proteins interact with other proteins by:
- interaction between the pre-folded domains
- new folding upon interaction of 2 proteins
- change in configuration or folding upon modifications such as phosphorylation or acetylation
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The protein 3D structure and RNA 3D structure can interact in specific manners such as:
- interaction of each tRNA with the specific enzyme that specifically links the correct amino acid to the correct tRNA
- Alternatively in other cases, it is possible that interaction of protein and RNA causes or stabilizes their folding.
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Almost all the processes in the cell from DNA and RNA polymerization to metabolism and generation and use of energy is accelerated by the activity of the __ as the biological catalysts.
enzymes
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enzyme facts
- required in small amounts
- not altered/consumed in rxn (or returned to their original status after the rxn)
- no effect on thermodynamics of rxn (does not supply E or determine product/reactants ratio)
- do accelerate rate of reaction (kinetics)
- highly specific for substrate/reactant
- very few side reactions (i.e. very "clean")
- subject to regulation
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To start any reaction, a __ is needed to push the molecules to the active state. Then if the reaction is accompanied with the __, it will go forward.
- small activation energy (EA);
- release of energy
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An enzyme __ EA. This is usually done by the __ of enzymes.
- lowers (so that ambient fluctuations of E are sufficient to start the reaction);
- active site
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A __ may interact with a domain other than the active site of the enzyme. If this interaction causes change of configuration in the protein and eventually the configuration of the active site, it may __. This type of regulating the activity of a protein is known as __
- ligand;
- induce or reduce the activity of the enzyme (depends on the type of change);
- allosteric regulation (not regulated by the real substrate or the analog of a substrate)
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example of allosteric regulation: A lac repressor (dimer protein) binds to a specific sequence of DNA.
- binding of allolactose (ligand) to the Lac repressor protein → change of configuration in the protein → its detachment from the DNA sequence
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