Quiz 3 Flashcards
Explain how fitness of a gene product affects mutations which lead to changes in primary structure?
If the mutation is deleterious or lethal in their effects, the mutation does not propagate. • If the mutation has no effect it can remain in the population. • If the mutation improves the fitness of the organism in its environment, it will be selected for and amplified in the population
hypervariable residue
Sequence positions that have no functional / structural role are free to mutate without affecting protein structure
invariant residue
Critical sequence positions required for function,or to maintain 3D structure, do not change
conservative residue
Some other sequence positions can only change to residues with similar chemical properties in order for the protein to remain physically similar
Describe the energetics that favour protein folding
∆Gsystem = ∆Hsystem -T∆Ssystem = -T∆Suniverse
ΔGsystem must be
Folding “orders” the polypeptide, decreasing entropy, leading to ΔSsystem
This must be offset by decreasing enthalpy (∆Hsystem
This adds disorder into the universe, increasing overall entropy (∆Suniverse > 0)
Protein folding is exothermic or endothermic?
exothermic, water molecules are released out of a locked conformation and have vibrational energy
native state of a protein
the fully folded state of that protein
how does a misfolded protein escape from a local energy well that is not its native state?
molecular chaperones
what proteins can fold on their own
ususally only small, soluble, globular proteins
at an extremely high level, what do molecular chaperones do?
Molecular chaperones add energy into the stalled folding process in a effort to push the protein over the activation energy barrier into a lower free energy minimum.
what are the two major families of molecular chaperones in eukaryotes?
Hsp70 (DnaJ is the bacterial homologue) and Hsp60
How did eukaryotic molecular chaperones get their names?
Hsp60 and Hsp70 (DnaK in bacteria) are “heat shock proteins”, named for the fact they are upregulated when cells briefly experience higher temperatures. Because heat denatures proteins, heat shock proteins attempt to rescue them and refold them correctly.
Hsp60
Heat shock protein 60 (Hsp60) is a mitochondrial chaperonin that is typically held responsible for the transportation and refolding of fully synthesized proteins from the cytoplasm into the mitochondrial matrix. In addition to its role as a heat shock protein, Hsp60 functions as a chaperonin to assist in folding fully synthesized linear amino acid chains into their respective three-dimensional structure. Through the extensive study of groEL, Hsp60’s bacterial homolog, Hsp60 has been deemed essential in the synthesis and transportation of essential mitochondrial proteins from the cell’s cytoplasm into the mitochondrial matrix.
Polypeptide initially binds to hydrophobic regions around the rim.
7 subunits, each binds ATP which elicits a conformational change and opens the recess for the rest of the protein to be pulled inside, after which the cap binds. Only one side of the barrel is occupied at any given time.
ATP is hydrolysed and the cap dissociates, the protein is released whether folded or not. Multiple cycles may be required to complete folding.
Hsp70
Hsp70 (bacterial homologue DnaK) binds to hydrophobic amino acids about 7 residues in length as the protein emerges from the ribosome they are being synthesized from.
Aided by Hsp40 (bacterial homologue DnaJ)
Uses ATP to ADP + Pi hydrolysis to initiate conformational change that locks Hsp70 tightly to polypeptide.
Hsp40 and ADP dissociate, binding of new ATP reverses conformational change releases folded polypeptide, process repeats.
What are the bacterial homologues to Hsp40 and Hsp60 and Hsp70?
- Hsp40* = DnaJ
- Hsp60* = GroEL
- Hsp70* = DnaK
Disulfide isomerase
Disulfide isomerases are chaperones that help many proteins form their correct disulfide bonds. Without these enzymes, initial folding may bring two Cys residues together that should not be bonded. Disulfide isomerase interchanges and shuffles these bonds until the correct disulfides are formed.
Peptide prolyl cis-trans isomerase
Peptide prolyl cis-trans isomerase (PPI) are chaperones that help in the conversion between trans and cis prolines
PPI
Peptide prolyl cis-trans isomerase (PPI) are chaperones that help in the conversion between trans and cis prolines
Protease
Proteases cleave off signal sequences, that target proteins to their cellular compartment, prosequences, that prevent a protein being active in the wrong cellular compartment, and secretion signals, that cause proteins to be secreted out of the cell.
List five molecular chaperones that aid protein folding
- Hsp60* (barrel and cap that act on fully synthesised proteins, uses ATP)
- Hsp70* (with Hsp40, acts on 7 hydrophobic amino acids as they exit the ribosome during translation, uses ATP)
- Disulfide isomerase* (corrects Cys S-S bonds)
- Peptide prolyl cis-trans isomerase* (PPI) (converts cis and trans prolines)
Proteases (generic term) (cleaves signal sequences, prosequences, and secretion signals)
signal sequence
A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.[1] These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, golgi or endosomes), secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, the majority of type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved.
prosequence
A protein precursor, also called a pro-protein or pro-peptide, is an inactive protein (or peptide) that can be turned into an active form by posttranslational modification. The name of the precursor for a protein is often prefixed by pro. Examples include proinsulin and proopiomelanocortin.
Protein precursors are often used by an organism when the subsequent protein is potentially harmful, but needs to be available on short notice and/or in large quantities. Enzyme precursors are called zymogens or proenzymes. Examples are enzymes of the digestive tract in humans.
secretion signal
A form of signal sequence that targets a protein for excretion: A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.[1] These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, golgi or endosomes), secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, the majority of type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved.
cofactor
an additional atom or molecule essential for protein structure/function
A cofactor is a non-protein chemical compound that is required for the protein’s biological activity. These proteins are commonly enzymes, and cofactors can be considered “helper molecules” that assist in biochemical transformations.
Cofactors can be subdivided into either one or more inorganic ions, or a complex organic or metalloorganic molecule called a coenzyme; most of which are derived from vitamins and from required organic nutrients in small amounts. A cofactor that is tightly or even covalently bound is termed a prosthetic group. Some sources also limit the use of the term “cofactor” to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is called a holoenzyme.
Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase at the junction of glycolysis and the citric acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide (FAD), and the cosubstrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg2+).
Organic cofactors are often vitamins or are made from vitamins. Many contain the nucleotide adenosine monophosphate(AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered a kind of “handle” by which the enzyme can “grasp” the coenzyme to switch it between different catalytic centers.
metal cofactor
the simplest cofactors, metal ions that bind directly to the protein.
can be involved in catalysis, in binding ligands, in electron transfer, can have structural role, or help neutralise highly charged biomolecules
different metals have different preferred protein ligands (generally N, O, or S) and adopt different geometries. Water (or hydroxide) generally occupies at least one ligand position
metals must come from diet
what roles can metal cofactors fufill?
can be involved in catalysis, in binding ligands, in electron transfer, can have structural role, or help neutralise highly charged biomolecul
what are the most common structural metal cofactors and why?
calcium (Ca2+), magnesium (Mg2+), zinc (Zn2+)
they are charge neutralising metals
(shown: X, Y are negative residues like D or E, stabilised in close proximity by Ca2+, which prevents charge repulsion between the residues)
organometallic cofactor
in-class example: Haeme group
cofactors in many proteins, most important of which are haemoglobin, myoglobin, cytochrome
consists of a porphyrin ring which may or may not be covalently bonded to the protein backbone.
synthesised enzymatically, disease results from dysfunction in its synthesis.
vitamin
All the water soluble vitamins are either coenzymes or are the raw material for the synthesis of coenzymes.
what is the difference between ligands and cofactors?
Ligand is a more general term refering to a compound that binds to a given enzyme. It could be a substrate, but also have regulatory roles, for instance. A cofactor refers specifically to a compounds that are part of an active enzyme.
what are the most common metal cofactors for catalysis and why?
Fe2+ and Fe3+
Cu2+ and Cu+
generally cofactors that can change their state easily
Although Zn2+ cannot change state, it is a good Lewis Acid (accepts electron pair) and plays a catalytic role in some enzymes
what are the most common metal cofactors for electron transfer and why?
Fe2+ and Fe3+
Cu2+ and Cu+
generally cofactors that can change their state easily
