Term
| why do we need to bind O2 to hemoglobin? |
|
Definition
| because the solubility of O2 in water is very low |
|
|
Term
| what is another way to describe the heme-heme interaction? |
|
Definition
|
|
Term
| what happens to hemoglobin if we are exposed to CO? |
|
Definition
| CO acts as a competitive inhibitor |
|
|
Term
| what happens in a rightward shift of the hemoglobin dissoc. curve? |
|
Definition
|
|
Term
| what is carbonic anhydrase? |
|
Definition
| enzyme that catalyzes reaction where CO2 +H2O forms H2CO3 and then biocarbonate. This occurs in RBCs |
|
|
Term
| do zwitter ions have high or low IM forces? why? |
|
Definition
| high due to H bonding and ionic bonding |
|
|
Term
|
Definition
|
|
Term
| what does catabolic mean? |
|
Definition
| ~cannabalize, so destroy, break apart |
|
|
Term
| if a protein exists as a single polypeptide chain does it have a quaternary structure? |
|
Definition
| No, quaternary structure implies multiple polypeptides |
|
|
Term
| what is the protein’s primary structures? |
|
Definition
| The AA sequence that is covalently linked together |
|
|
Term
| what is the protein’s secondary structure? |
|
Definition
| Alpha helices or beta sheets or flexible areas that are neither |
|
|
Term
| does the secondary structure involve side chains? |
|
Definition
| It does NOT involve side chains, however the secondary structure can be influenced by side chains |
|
|
Term
| is proline likely to be found in an alpha helix? |
|
Definition
|
|
Term
| what is a protein’s tertiary structure? |
|
Definition
| Folding pattern of a single polpeptide chain |
|
|
Term
| what influences tertiary structure? |
|
Definition
| Main and side chain H bonds, ionic interactions, van der waals interactions, hydrophobic interactions |
|
|
Term
| what adds stability to tertiary interactions? |
|
Definition
| Disulfide bonds between cysteine residues |
|
|
Term
| what is the proteins quaternary structure? |
|
Definition
| Interactions between polypeptide chains |
|
|
Term
| what influences quaternary structure? |
|
Definition
| Main and side chain H bonds, ionic interactions, van der waals interactions, hydrophobic interactions |
|
|
Term
| what is an important feature of quaternary structure? |
|
Definition
| The relative subunits can change to regulate a protein’s function—ex. Hemoglobin |
|
|
Term
| what is the main role of quaternary structure? |
|
Definition
|
|
Term
| what are the non-covalent interactions that are important for proteins? |
|
Definition
| H bonds, ionic interactions, van der waals interactions, hydrophobic interactions |
|
|
Term
| what are the kinds of H bonds found in proteins? |
|
Definition
| Between main chains, between side groups, between side groups and main chains |
|
|
Term
| what is an ionic interaction? |
|
Definition
| A salt bridge, basically charged groups that are attracted or repelled by each other |
|
|
Term
| what are hydrophobic interactions? What do they effect? |
|
Definition
| They are interactions that have a tendency to want to exclude water and are driven by entropy concerns |
|
|
Term
| What are Van der Waals forces? |
|
Definition
| Any 2 atoms in close proximity, can gain binding E as a result |
|
|
Term
| Why do we say that the peptide bond has a double bond character? |
|
Definition
| Because the bond is actually shorter than a single bond and can exist as a double bond 1/3 of the time because of the delocalized electrons that move from the amine N to the carbonyl C |
|
|
Term
| What are the consequences of the peptide bond having double bond properties? |
|
Definition
| 1. The bond can become planar, so there is restricted rotation around the bond itself which removes complexity from the system, 2. The bond has a polarity ( - at O, + at N) which makes it a good candidate for H bonding), 3. There are delocalized electrons which makes the carbon less susceptible to hydrolysis |
|
|
Term
| What is the steric configuration of most peptide bonds? |
|
Definition
|
|
Term
| What is the only AA that is found in a cis conformation? |
|
Definition
|
|
Term
| Where is rotation possible in the peptide chain? |
|
Definition
| Before or after the alpha carbon |
|
|
Term
| What is the name of the angle before (closer to the N) side of the alpha carbon? |
|
Definition
|
|
Term
| What is the name of the angle after (closer to the COO) side of the alpha carbon? |
|
Definition
|
|
Term
| Are all conformations and bond angles allowed in peptide chains? |
|
Definition
| No because there can be a steric clash between the COO and amino N if they rotate too much |
|
|
Term
| What does a Ramachandran Plot show? |
|
Definition
| That the values for phi and psi are restricted and that the alpha helix and beta sheet are heavily favored |
|
|
Term
| In an alpha helix H bonds occur every ______ residue |
|
Definition
|
|
Term
| In an alpha helix H bonds occur between? |
|
Definition
| The carbonyl O and the amino H |
|
|
Term
| The alpha helix turns every _____ residues? |
|
Definition
|
|
Term
| What determines which 2dary structure forms? |
|
Definition
|
|
Term
| In an alpha helix are all the H bond opportunities satisfied? |
|
Definition
|
|
Term
| An alpha helix is favorable in what environment? |
|
Definition
| Lipid bilayer. No h bonds need to interact with the water because they are all satisfied, so basically you are masking the polarity |
|
|
Term
| In an alpha helix the R groups are oriented where? |
|
Definition
| To the outside of the helix, i.e. away from the core |
|
|
Term
| What are amphipathic helices? |
|
Definition
| Helices that are arranged so that one side is hydrophilic and one side is hydrophobic |
|
|
Term
| Why are alpha helices used to span membranes? |
|
Definition
| All of the H bonds are satisfied so you mask the polarity |
|
|
Term
| Do all the AA sequences form secondary structure? |
|
Definition
| NO, there can be lops or entirely unstructured regions. Protein structure is often secondary structure connected by flexible segments |
|
|
Term
| Can beta sheets be found across membranes? |
|
Definition
| Yes, although that’s less common. Same idea, have all the H bonds satisfied |
|
|
Term
| What is the name of a large class of signaling receptors with multiple helices? |
|
Definition
| G-protein coupled receptors |
|
|
Term
| What kinds of process are GPCRs (G protein coupled receptors) involved in? |
|
Definition
| smell, taste, vision, neurotransmission, hormone signaling, BP control, developmental processes |
|
|
Term
| What is the main difference between beta sheets and alpha helices? |
|
Definition
| Beta sheets have H bonds that occur between different strands and are farther apart than the H bonds in alpha helices. |
|
|
Term
| What are the two orientations beta sheets can have? |
|
Definition
| Parallel and anti-parallel |
|
|
Term
| Are all of the H bonds satisfied in beta sheets? |
|
Definition
| No, only those on the interior of the sheets, the outer strands can H bond in tertiary structure |
|
|
Term
|
Definition
| Aggregates that are mostly formed from beta sheets |
|
|
Term
| What is the role of a beta turn? |
|
Definition
| To connect 2 beta strands or 2 alpha helices |
|
|
Term
| What are beta turns stabilized by? |
|
Definition
|
|
Term
| Ionic and Van der Waals have what effects on tertiary and quaternary structure? |
|
Definition
| They stabilize tertiary structure and mediate quaternary structure |
|
|
Term
| What is the strongest force that drives protein folding? |
|
Definition
| Hydrophobicity, driven by entropy concerns |
|
|
Term
| Why would a protein have hydrophobic residues on its exterior? |
|
Definition
| Because it will become an intramembrane protein |
|
|
Term
| Why is protein folding important? |
|
Definition
| So that proteins can ultimately do their function. Misfolding can cause to serious neurodegenerative illnesses |
|
|
Term
| What are conserved protein sequences? |
|
Definition
| Evolutionarily conserved regions, that are often very important for function |
|
|
Term
| How can we identify conserved protein sequences? |
|
Definition
| All possible comparisons are performed, and the ones with the highest number of matches are examined. The number that match is the proteins’ score |
|
|
Term
| There is usually some degree of similarity between proteins of the same _____? |
|
Definition
|
|
Term
| What are gaps used for in terms of comparing proteins? |
|
Definition
| Used to enhance alignment, i.e. to make one protein sequence as long as another one |
|
|
Term
|
Definition
| An independently-folding region of a protein |
|
|
Term
|
Definition
| A shorter sequence, usually part of a domain that has a particular function but might not be able to fold independently |
|
|
Term
| What determines the number of interaction partners a protein can have? |
|
Definition
| The number of functional domains. Some proteins are very specific while others are more promiscuous. |
|
|
Term
| Why might we mutate a protein sequence? |
|
Definition
| To see whether or not an alteration of an AA sequence will likely affect protein function |
|
|
Term
|
Definition
| A small molecule that non-covalently interacts with another protein |
|
|
Term
| What is the Kd and binding affinity? |
|
Definition
| The binding affinity refers to how long a ligand will bind to a protein, and the Kd is the concentration of the ligand at which half of the protein is bound to ligand. |
|
|
Term
| What is the relationship between Kd and binding affinity? |
|
Definition
| As the binding affinity goes up, the Kd goes down. |
|
|
Term
| Is the on rate similar among ligands? |
|
Definition
| Yes because it is mostly regulated by diffusion |
|
|
Term
| Is the off rate similar for ligands? |
|
Definition
| Not necessarily, because depends on affinity |
|
|
Term
| Why would we want a high or low Kd? |
|
Definition
| Depends if you want to transport or store ligands (ex. Myoglobin vs. hemoglobin) |
|
|
Term
| What is the half life of a medium Kd? |
|
Definition
|
|
Term
| What is the half life of a low Kd? |
|
Definition
|
|
Term
| As we increase the amount of ligand what can we ensure? |
|
Definition
| That all the protein has ligand bound to it |
|
|
Term
| Small changes in delta G, the free energy, lead to what kind of changes in the Kd? |
|
Definition
| HUGE ones. Since the relationship between the two is exponential |
|
|
Term
| Can adding 1 H bond change the Kd? |
|
Definition
| Yes, it can change it a lot |
|
|
Term
| What is the strongest interaction in terms of increasing bindng affinity? |
|
Definition
|
|
Term
| What is the weakest interaction in terms of increasing bindng affinity? |
|
Definition
| Van der Waals interations |
|
|
Term
| Binding affinity is the consequence of what? |
|
Definition
| Molecular interactions. When these go up, so does the binding affinity. |
|
|
Term
| What is a low Kd good for? |
|
Definition
| A long lived interaction (ex. Antigen-antibody) |
|
|
Term
| What is a high Kd good for? |
|
Definition
| A reversible interaction (ex. Hemoglobin and oxygen) |
|
|
Term
| what is the difference between deltaG, G '0 and G with the transition sign? |
|
Definition
delta G is the free energy
-delta G'0 is the delta G at standard temperature
-delta G transition sign is the delta G at the transition state. |
|
|
Term
| why might a reaction not occur even if the delta G for the reaction is negative? |
|
Definition
| because the reaction is not kinetically favored |
|
|
Term
| what is true when delta G = 0 |
|
Definition
| the reaction is at equilibrium |
|
|
Term
| how do enzymes accelerate the rate of chemical reactions? |
|
Definition
| they stabilize the transition state and reduce the activation energy via bonding interactions. basically they make a smoother energy path for the reaction to follow |
|
|
Term
| how would you draw a free energy diagram for an uncatalyzed and an enzyme-catalyzed reaction |
|
Definition
uncatalyzed: Ea is higher
catalyzed: Ea is lower, and there are two dips, one for the enzyme and substrate complex (ES) and another for the enzyme product complex (EP) |
|
|
Term
| what does the active site of the enzyme do? |
|
Definition
| it binds to the substrate and is the place where the reaction takes place |
|
|
Term
| Why enzymes have the highest binding affinity for the transition state of a reaction |
|
Definition
| enzymes have a higher binding affinity for the transition state because if it had a higher binding affinity for the substrate it would increase the Ea. By binding better to the transition state, which is in a higher energy state, it can ensure that the reaction goes to completion and that there is room for the products to form. Basically it wants to lower the energy of the transition state, not the substrate. |
|
|
Term
| what is the definition of an enzyme cofactor? |
|
Definition
| an enzyme cofactor is a non-protein molecule that speeds up the reaction of an enzyme (ex. is a metal or a vitamin) ex. Mg2+ in transcription |
|
|
Term
| what are the features that determine substrate specificity for enzymes? |
|
Definition
| Complementary shape, charge and hydrophilic/hydrophobic characteristics of enzymes and substrates are responsible for specificity. |
|
|
Term
| are enzymes altered during reactions? |
|
Definition
|
|
Term
What is the Michaelis-Menton equation?
How does it simplify at high and low concentrations |
|
Definition
Vo = vmax * [S] / [S] + Km
at high concentrations Vo = vmax
at low concentrations Vo is proportional to substrate
when [S] = Km, Vo = 1/2 v max |
|
|
Term
what is the Km?
how can we find the value experimentally? |
|
Definition
the Km is the amount of substrate that leads to the enzyme having 50% binding or 50% rxn rate
Find the max rxn rate, then find the 1/2 rxn rate and measure the substrate concentration at that rate |
|
|
Term
what is the Vmax?
how can we find this value experimentally? |
|
Definition
the maximum rate that a catalyzed reaction can have
-saturate the enzyme with substrate and see how fast it goes |
|
|
Term
|
Definition
| the kcat is the rate constant for a catalyzed reaction. It regulates how fast the reaction can take place. |
|
|
Term
| How can we find out the value of Kcat experimentally? |
|
Definition
we can find the vmax of a catalyzed reaction with known enzyme concentration.
vmax = [Et] * kcat. |
|
|
Term
| How does the Km relate to the substrate's affinity for the enzyme? |
|
Definition
| the lower the Km, the greater the substrate's affinity for the enzyme |
|
|
Term
what is the difference between irreversible, reversible, competitive, noncompetitive and mixed
inhibitors? |
|
Definition
irreversible: covalently bound, permanently stuck
reversible: can come unbound
competitive: bind at active site
non-competitive: bind at a site that is not the active site, doesn't inhibit substrate binding
mixed: bind at a site that is not the active site, decreases substrate binding |
|
|
Term
How does a competitive inhibitor change a velocity plot?
double reciprocal plot? |
|
Definition
-Km changes and Vmax is the same (although probably never reached)
-y intercept (1/vmax) is the same, but the Km is higher, so the x intercept is closer to 0 |
|
|
Term
How does a noncompetitive inhibitor change a velocity plot?
double reciprocal plot? |
|
Definition
-the Km is the same but the vmax is MUCH lower
-y intercept (1/vmax) is higher, but the Km stays the same (bc the active site has the same binding affinity) |
|
|
Term
How does a mixed inhibitor change a velocity plot?
double reciprocal plot? |
|
Definition
graph is similar to a non-competitive, however it doesn't flatten out as early
-y intercept is higher (vmax is lower) and the kM is higher |
|
|
Term
| How to draw substrate velocity curves for allosteric vs. non-allosteric enzymes |
|
Definition
| allosteric enzymes have sigmoidal substrate-velocity curves because they have cooperative binding just like hemoglobin. they are usually multiunit enzymes that are regulated by the binding of other molecules |
|
|
Term
How substrate-velocity curves for allosteric enzymes will change in the presence of an
activator or inhibitor |
|
Definition
In the presence of an activator, the curve will move up and to the left. activators will stabilize the conformation of the enzyme that has a higher affinity for the substrate.
in the presence of an inhibitor, the curve will move down and to the right. |
|
|
Term
| How can post-translational modifications such as phosphorylation and proteolysis regulate enzyme activity? |
|
Definition
kinases are often regulated by phosphorylation
proteases are often modified by proteolysis, so they are activated once they reach their destination, and are turned on. They are not turned on where they are synthesized. |
|
|
Term
| why is the Kd tailored to a biological context? i.e. why/when would we want tight binding vs. loose binding |
|
Definition
low Kd--good in situations when we want something to last a long time (ex. antibodies and antigens)
high Kd--good for situations when we want something to be reversible (ex. hemoglobin) |
|
|
Term
| what are the chemical differences between RNA and DNA? |
|
Definition
-RNA contains Uracil and DNA contains Thymine
-RNA is generally single stranded, DNA is double stranded (not sure this counts as chemical)
-RNA contains the sugar ribose, DNA contains the sugar 2' deoxyribose |
|
|
Term
| What are the differences between the organization of prokaryotic and eukaryotic genes? |
|
Definition
Prokaryotic DNA is circular, and does not have histones, and is not formed into chromosomes. Prokaryotes also have DNA in plasmids which are used to infect host cells.
Eukaryotic DNA is located on chromosomes in the nucleus of the cell and contains histones. |
|
|
Term
| what is the functional role of mRNA? |
|
Definition
| mRNA provides a code for amino acids that is read by tRNAs |
|
|
Term
| what is the functional role of rRNA? |
|
Definition
| rRNA comprises the catalytic component of the ribosomes |
|
|
Term
| what is the functional role of tRNA? |
|
Definition
| tRNA reads the mRNA code and transfers a corresponding amino acid to the growing polypeptide chain |
|
|
Term
| what is the functional role of snRNA? |
|
Definition
| snRNA comprises the subunits of the spliceosomes which are used to remove introns from pre-mRNA |
|
|
Term
| what is the function of the RNA polymerase? |
|
Definition
| the function of the RNA polymerase is to bind to the DNA, unwind it and synthesize RNA using DNA as a template |
|
|
Term
| what is the basic mechanism of transcription? (basic steps) |
|
Definition
| 1) RNA Polymerase binds to the promoter sequence of the DNA (with general transcription factors) 2) the polymerase unwinds the DNA, forming a transcription bubble and feeds the DNA through its active site 3) the polymerase synthesizes RNA using ribonucleotide triphosphates in a 5' to 3' direction |
|
|
Term
| what are the distinct functions of the general and regulatory transcription factors? |
|
Definition
general transcription factors bind to all promoters that are transcribed by RNA polymerase II and recruit the polymerase. Without the general transcription factors, RNA will not be synthesized. Together, and with the additon of other proteins such as a helicase, these proteins form the preinitiation complex.
Regulatory transcription factors are needed to move from initiation to elongation. They regulate the rate of transcription, and they bind to specific DNA sequences to activate or repress them. They also recruit polymerases back to the DNA so the gene will be re-transcribed |
|
|
Term
| How do proteins recognize specific DNA sequences? |
|
Definition
most proteins bind to the DNA at the major groove (more binding energy and more space) and use protein motifs to regonize DNA binding domains. i.e. the proteins recognize short DNA sequences
2 examples of protein motifs are: leucine zipper and zinc finger. These motifs have specific amino acids that interact with the bases in the DNA. |
|
|
Term
|
Definition
| the TATA box is a consensus sequence that is enriched for Ts and As and is located upstream of the transcription start site. It is part of the promoter region, and recruits general transcription factors to DNA |
|
|
Term
| how is the TATA box important for the transcription of DNA? |
|
Definition
the TATA box is important for transcription because it:
-recruits the general transcription factors to DNA, which recruits the polymerase
-bends DNA which allows certain TFs (transcription factors) to bind
-once Polymerase binds, the TATA box recruits more TFs that are necessary for transcription (ex. helicase) |
|
|
Term
| what are the functions of coactivators and corepressors? |
|
Definition
proteins that up regulate or down regulate transcription factors by binding to their activation domain. (they do not directly bind to DNA)
additonal way that transcription can be controlled |
|
|
Term
| what are the different types of co-activators and co-repressors? |
|
Definition
-can act as a landing pad for other coactivators/repressors
-can be enzymes, ex. CREB which has acetyl transferase activity, or HATs or HDAC which control acetylation of histones and access to DNA
-hormones |
|
|
Term
| what is a control region? |
|
Definition
| the DNA sequence that recruits regulatory transcription factors |
|
|
Term
| How do different transcription factors work together to control transcription? |
|
Definition
| Many trasncription factors can be activated or repressed, the aggregate of these signals is often coordinated by the mediator complex which either stimulates or represses transcription |
|
|
Term
| How can regulatory transcription factors be regulated? |
|
Definition
-by co-activators or co-repressors that bind to the active domain of the transcription factor
-extent to which the transcription factors are present in different cell types
-they can also be regulated by signaling pathways |
|
|
Term
| What are some of the mechanisms by which transcription factors are regulation? |
|
Definition
ex. CRB (binds to TF CREB) coactivator, which has acetyltransferase activity and can stimulate transcription
ex. coactivators that act as landing pads for other coactivators/repressors (ex. CBP)
-transcription factors can bind cofactors that acetylate histones
-transcription factors can be phosphorylated or not, which either allows them to bind a cofactor, or blocks this ability
-ex. hormones can be part of signaling pathways that allow TFs to move throughout the cell to the proper destination
(not sure this is a complete answer) |
|
|
Term
| What is the mediator complex? |
|
Definition
a coactivator that binds to the active domain of the TFs and mediates signals from many transcription factors to the RNA polymerase. It's sort of the RNA polymerase's secretary.
It can phosphorylate the RNA polymerase to stimulate activity |
|
|
Term
How can histones be post-translationally modified?
How does this affect chromatin structure? |
|
Definition
-chromatin remodeling proteins can move the histones around (not sure if this counts as modification)
-repressor transcription factors (HDACs) bind, methylates the chromatin tails, then other proteins bind that form heterochromatin
-activators (HATs) bind and acetylate the histone tails, cofactors bind, and the DNA is unwound, becomes euchromatin
effect on chromatin structure is either that it is densely packed (heterochromatin) or unwound (euchromatin) |
|
|
Term
| where do repressos start deacetylating DNA? |
|
Definition
| near the TATA box, block the general transcription factors from binding (can't bind if the histones are acetylated) |
|
|
Term
| What are nuclear hormone receptors? |
|
Definition
| these are essentially transcription factors that have an additional binding site for hormones |
|
|
Term
| How is the activity of nuclear hormone receptors regulated? |
|
Definition
| in the presence of a hormone the receptors are activated, and deactivated when no hormones are present |
|
|
Term
| what is the basic structure of eukaryotic pre-mRNA and mature mRNA? |
|
Definition
pre-mRNA contains introns and exons
mature mRNA contains only exons, and also has a 5' cap and a poly A 3' tail |
|
|
Term
| what are the key types of pre-mRNA processing? how are they coupled to transcription? |
|
Definition
capping, splicing, and polyadenylation
these processes occur in the order listed above, and occur co-transcriptionally, as soon as each exon is transcribed. proteins responsible for this processing bind to the C terminal of the RNA polymerase via phosphorylation. |
|
|
Term
| what is the function of the 5' cap? |
|
Definition
-prevent mRNA degradation
-signals to ribosomes that the mRNA is ready to be translated
-labels mRNA for export from the nucleus. |
|
|
Term
| what is the function of the spliceosome? |
|
Definition
|
|
Term
| where are the conserved sequence elements required for splicing located? |
|
Definition
| they are usually located at the 3' and 5' ends of the intron. Additionally a branch site (an adenine) located near the 3' end of the intron is necessary for splicing. The first two sites span the intron and exon. |
|
|
Term
| How are the 5' and 3' splice sites defined? |
|
Definition
|
|
Term
| What are decoy splice sites? |
|
Definition
| Sites in the introns that look like splice sites (i.e. have the consensus sequence) but are not located at the boundary between exons and introns |
|
|
Term
| what is a snRNP composed of? |
|
Definition
|
|
Term
| what are the functions of the U1 and U2 snRNPs in splice site recognition? |
|
Definition
| the U1 snRNP recognizes the 5' site and the U2 snRNP recognizes the 3' splice site and the branch site. They also recruit other snRNPs |
|
|
Term
| What is the function of exon-junction complexes? |
|
Definition
| these bind to the mRNA during splicing and facilitate export of the mRNA from the nucleus. They are eventually exchanged for translation initiation factors |
|
|
Term
| What is the function of SR proteins? |
|
Definition
| SR proteins get the U1 and U2 snRNPs to the correct sites, i.e. enhance exon recognition. They stabilize the formation of the U1, U2 complex by having multiple protein-mRNA interactions. |
|
|
Term
| how are exons defined by the splicing machinery and the significance of the exon definition model |
|
Definition
exons are defined by ESE (exon splicing enhancer) regions in the DNA that bind/recruit SR proteins.
the significance of the exon model is that exons are short and introns are very large, and the splicing sequences are short. Sooo they wouldn't work very well on introns. |
|
|
Term
| How can alternative splicing give rise to different protein isoforms? |
|
Definition
| because not all exons are spliced all the time. this can lead to changes in the location and expression levels of proteins (however mutations that affect alternative splicing can cause disease) |
|
|
Term
| what is the role of ESEs (exon splicing enhancers)? |
|
Definition
| they are the regions in the exons that bind to SR proteins to encourage splicing |
|
|
Term
| what is the role of ESSs (exon splicing silencers)? |
|
Definition
| they repress splice sites or enchancers |
|
|
Term
| HOw can alternative splicing be regulated? |
|
Definition
| by ESEs, ESSs, and by phosphorylation of SR proteins (if they are phosphorylated, exon will be included, but if the SR protein is dephosphorylated then it won't be included) |
|
|
Term
| what are the consequences of mutations in sequences required for splicing? |
|
Definition
| most common result is exon skipping, but can also have exons extended, or have completely new exons |
|
|
Term
| how is splicing coupled to mRNA export? |
|
Definition
mRNA will not be exported from the cell until the introns have been spliced out?
*not sure if this is correct |
|
|
Term
| what is the function of the polyA tail and how is it constructed? |
|
Definition
the polyA tail's function is to stabilize mRNA and facilitate its exit from the nucleus
it's is constructed similar to the spliceosome, many proteins are recruited, splice mRNA at recognition site and add a polyA tail with an enzyme that is about 250 nucleotides long |
|
|
Term
| how are micro RNAs generated? |
|
Definition
|
|
Term
| how do micro RNAs regulate gene expression? |
|
Definition
| they operate in all nucleated cells to regulate gene expression by cleaving mRNA. microRNAs are regulated by signaling pathways |
|
|
Term
| what are the differences between microRNAs and siRNAs? |
|
Definition
| siRNAs are delivered exogenously whereas microRNAs are delivered endogenously |
|
|
Term
| what is meant by the genetic code being universal? |
|
Definition
| it is the same in all organisms |
|
|
Term
| what is meant by the genetic code being specific? |
|
Definition
| the same codon always codes for the same amino acid |
|
|
Term
| what is meant by the genetic code being redundant? |
|
Definition
| many codons can code for the same amino acid |
|
|
Term
| what is meant by the genetic code being commaless? |
|
Definition
| there is no space between codons in the RNA |
|
|
Term
| what is meant by the genetic code being non-overlapping? |
|
Definition
| codons do not overlap in the RNA |
|
|
Term
| how does a silent mutation affect the primary protein sequence? |
|
Definition
| it doesn't. it still codes for the same amino acid |
|
|
Term
| how does a missense mutation affect the primary protein sequence? |
|
Definition
| it changes the codon to code for a different amino acid |
|
|
Term
| how does a nonsense mutation affect the primary protein sequence? |
|
Definition
| instead of coding for an amino acid it codes for a stop sequence |
|
|
Term
| how does a frameshift affect the primary protein sequence? |
|
Definition
| if it inserts a number of nucleotides that is not divisible by three, it alters the reading frame, which will likely cause many missesnses or a nonsense. |
|
|
Term
| what are the general properties and functions of tRNA? |
|
Definition
properties: made up of ribonucleases into a T structure (3d structure is an L), most of nucleotides are base paired to each other, but not at anti-codon loop or at 3' end, which binds to amino acid (AA).
functions: to interpret the genetic code on mRNA and develop a polypeptide chain that corresponds to the code |
|
|
Term
| how do aminoacyl-tRNA synthetases ensure accurate charging of tRNAs? |
|
Definition
the synthetases have an active site and an editing site. If the wrong AA is added to the synthetase, it will bind to the editing site and be released. Only the correct amino acid can attach to the active site. Additionally there are many binding sites between the tRNA and the synthetase.
Additionally they recognize many sites on the tRNA, not just the codon, which increase the fidelity of the synthetase |
|
|
Term
| what are the main properties and functions of ribosomes? |
|
Definition
they are made up of two subunits, and have tunnels and channels to accomodate tRNA, mRNA and the growing polypeptide chain.
They bind to the mRNA and provide the space for translation and aide translation by stabilizing correct pairings between tRNA and mRNA. the ribosome has three locations tRNAs move through as they translate the mRNA into protein |
|
|
Term
| how do ribosome monitor the accuracy of anticodon-codon interactions? |
|
Definition
the ribosomal subunit stabilizes CORRECT base pairs between the tRNA and mRNA (only works at positions 1 and 2, not the wobble position)
if the base pairs are not correct, the tRNA will dissociate |
|
|
Term
| what are the steps in protein synthesis that require energy? |
|
Definition
1) Forming the adenylated amino acid
2) Charging the tRNA with the amino acid
3) bringing tRNAs to ribosome
4) moving the ribosome down the mRNA
5)in eukaryotes, termination requires GTP |
|
|
Term
| How do G proteins function as molecular switches? |
|
Definition
because the G protein can only act on certain proteins when it is in a certain conformation, and it has a different conformation when bound to GTP then when it's bound to GDP. It is a very poor enzyme, so it needs GAP to hydrolyze GTP and GEF to bind new GTP.
ex. is with IF2 in prokaryotes. IF2 is a G protein that chaperones fMet tRNA to the P site during initiation, prevents hydrolysis of this tNRA, and helps the large ribosomal subunit bind. After the tRNA is delivered and the full ribosome is assembled, it will be hydrolyzed, change conformations and release from the tRNA. |
|
|
Term
| What is the role of GTP hydrolysis in initiation and elongation? |
|
Definition
Basically GTP hydrolysis signals that initiation is complete and elongation can begin because the full unit has assembled and the first tRNA is in the P site.
GTP is also part of the EF-Tu (which is similar to IL2 but for elongation) that chaperones tRNAs to the A site. However the GTP will not hydrolyze until the tRNA has been read. There are two time delays: EF-Tu has to hydrolyze GTP and it has to dissociate from the tRNA |
|
|
Term
| What is kinetic proofreading? |
|
Definition
| incorrect base pairs will have a high Kd and preferentially dissociate before EF-Tu has dissociated or before it has hydrolyzed GTP. Correct base pairs will have a low Kd and stay bound |
|
|
Term
| How is protein translation regulated in eukaryotes? |
|
Definition
1. regulate initiation factors
2. regulate by requiring certain sequences in 5' and 3' regions, ex. phosphorylate parts of the UTRs that block initiation complex or phosphorylate EF-Tu so it can't regenerate GTP
3. hairpin structures in 5' UTR can block ability of 40S subunit to move along mRNA and bind to AUG
4. micro RNAs can block the 3' UTR and block translation |
|
|
Term
| what are the differences between prokaryotic and eukaryotic protein synthesis? |
|
Definition
-prokaryotes have a shine-dalgarno sequence that tells the initiation factors where to bind (their mRNA is polycistronic, so there will be many such sequences along the mRNA)
-prokaryotes have smaller ribosomes
-in prokaryotes translation can occur co-transcriptionally
-eukaryotes form a pre-initiation complex. the first tRNA is on the complex before it binds mRNA (in prokaryotes, mRNA is bound first)
-in eukaryotes, termination involves GTP |
|
|
Term
| what is the function of polysomes? |
|
Definition
| they are proteins that bind to the polyA tail and also bind to initiation factors at the 5' end to form a loop, which is a stable complex that allows the ribosomes to readily reform after they finish one round of translation |
|
|
Term
| how do protein synthesis inhibitors serve as antibiotics? |
|
Definition
because they are targeting protein synthesis in bacteria (prokaryotes)
they inhibit the binding of tRNAs, cause misreading of mRNA, inhibit peptidyl transferase activity, and block the AA chain from exiting the ribsome |
|
|
Term
| what is the difference between a peptide bond and an isopeptide bond? |
|
Definition
peptide bond occurs between main chain of amino acids
isopeptide bond occurs between the C terminus of an amino acid and the side chain of a lysine |
|
|
Term
| why does the ubiquitination of a protein require ATP? |
|
Definition
| because you are creating a high energy bond, after this point the enzymatic reactions are energetically favorable |
|
|
Term
| why does the degradation of a ubiquitinated protein by the proteasome require ATP? |
|
Definition
| ATP is needed to move the protein poly peptide chain from the regulatory particle (RP) to the core particle (CP) |
|
|
Term
| what are examples of proteins that are degraded by the ubiquitin pathway? |
|
Definition
| misfolded proteins, cyclin B, which needs to degrade in order for the cell cycle to advance |
|
|
Term
| what are the steps in degradation of a ubiquitinated protein by the proteasome? |
|
Definition
1) RP recognizes protein with ubiquitin
2) RP opens gate to CP, starts to translocate protein
3) RP proteins continue to unfold and translocate protein using APT
4) simultaneously RP removes ubiquitin from protein
5) CP cleaves protein and releases oligopeptides |
|
|
Term
| what is the role of the E1 enzyme class in the ubiquitin pathway? |
|
Definition
| activate ubiquitin and form a high energy bond |
|
|
Term
| what is the role of the E2 enzyme class in the ubiquitin pathway? |
|
Definition
| transfer the ubiquitin to the E2, which can interact with the substrate |
|
|
Term
| what is the role of the E3 enzyme class in the ubiquitin pathway? |
|
Definition
| bring the E2 and substrate together so that the ubiquitin can be transfered to the lysine |
|
|
Term
| what is the function of the regulatory particle (RP)? |
|
Definition
-recruits ubiquitinated proteins
-controls protein entry to CP and unwinds protein
-removes ubiquitin |
|
|
Term
| what is the function of the core particle (CP)? |
|
Definition
| -to degrade the protein (i.e. to cleave it) |
|
|
Term
| how can the degradation of the substrates of the ubiquitin-proteasome pathway be regulated? |
|
Definition
-variation in kinds of ubiquitin chains can lead to different fates for different proteins
-can regulate the E3 enzymes, inactivate them in certain environments
-can phosphorylate the substrate |
|
|
Term
| how is the substrate specificity for the ubiquitin proteasome pathway determined? |
|
Definition
|
|
Term
| how does the proteasome differ from typical proteases like trypsin? |
|
Definition
| active sites are on the interior and ATP is required |
|
|
Term
| how do storage lipids differ from membrane lipids? |
|
Definition
storage lipids are triacylglycerols: made up of glycerol and fatty acid tails and are NON-POLAR
membrane lipids are made up of a polar or charged domain (usually phosphate or sugar) and are POLAR |
|
|
Term
| what is the difference between glycerophospholipids and sphingolipids? |
|
Definition
glycerophospholipids bind 2 fatty acid tails
sphingophospholipids only bind one fatty acid because they already contain a lipid tail. They bind fatty acids via amines not esters, no phosphates are used to attach head groups, so the lipids are neutral. Can also bind complex sugars (used to form antigens) |
|
|
Term
| what is the difference between PIP2, PIP3 and IP3? |
|
Definition
PIP2: part of cell membranes, signaling molecule (2 sites phosphorylated)
PIP3: downstream signaling molecule (3 sites phosphorylated)
I3: molecule that can enter the membrane (3 sites on sugar phosphorylated) |
|
|
Term
| what is the difference between how PIP2, PIP3 and IP3 are generated by phosphatidylinositol? |
|
Definition
PIP2: generated when 4' and 5' sites are converted from OH to phosphate groups
PIP3: generated when the 3' OH group on PIP3 is phosphorylated
IP3: generated when PIP2 is cleaved between sugar and lipid, 1' carbon retains phosphate group |
|
|
Term
| what is the role of cholesterol in the membrane? |
|
Definition
| modulates fluidity and permeability. The more cholesterol, the stiffer the membrane, interacts with the fatty acid tails. The hydroxyl tail of cholesterol will be closer to the glycerol part of the phospholipids. |
|
|
Term
| what are the differences and similarities between the three classes of proteins that confer selective permeability? |
|
Definition
-pumps, channels and transporters
-generally moving something down its concentration does not require energy.
-moving something against its concentration does require energy, either in the form of ATP or from energy generated by moving another molecule down its concentration gradient
-the rate can be fast or slow, depending on the Kms of the substrates for the proteins
-these are all selective for certain types of ions and molecules |
|
|
Term
| what is the resting electrical potential of the cell? |
|
Definition
|
|
Term
| what are the relative concentrations of sodium and potassium inside and outside of the cell? |
|
Definition
sodium is high outside of the cell, low inside
potassium is low outside of the cell, high inside |
|
|
Term
| how is the asymmetry of the relative concentrations of sodium and potassium generated? |
|
Definition
Na/K ATPase transfers 3 Na+ out of the cell for every 2 K+ that enter.
(without the ATPase, this asymmetry wouldn't exist) |
|
|
Term
| HOw does the action of the Na/K ATPase and selective permeability of potassium underlie the intracellular negativity of the transmembrane potential? |
|
Definition
| The membrane is only permissible to K+. K flows down it's concentration gradient, however since other ions cannot flow through the K channels, K will stop flowing once the electrical gradient opposes further movement of K+ down its concentration gradient. |
|
|
Term
| How is the membrane potential used by carriers and channels for transport and signaling? |
|
Definition
some channels are voltage gated, so they only open when the membrane potential reaches a certain point.
Also used by cells to detect build up of certain ions that they want to get rid of. Ex when glucose builds up, so does ATP in the cell. Increased ATP blocks the potassium channel, so membrane becomes more positive, which opens Ca+ channels. Ca+ floods into cell, which triggers vesicles full of insulin to bind to the membrane |
|
|
Term
| what are the possible destinations of proteins within the cell into different compartments? |
|
Definition
| cytoplasm, nucleus, mitochondria, membrane, ER/Golgi or secreted |
|
|
Term
| what is a nuclear localization sequence? what is its function? |
|
Definition
| it is a short linear sequence on the surface of the protein (protein doesn't need to unfold). Function is that it is needed so that import receptors to the nucleus recognize and bind to the protein. the more sequences there are on the protein, the faster it will be imported |
|
|
Term
| what is the function and definition of a nuclear export sequence? |
|
Definition
| a leucine rich ~10 amino acid sequence. sometimes molecules that need to exit the nucleus bind to proteins that contain an NES, which is a signal that designates the protein for export |
|
|
Term
| what is the function and definition of a protein signal sequence? |
|
Definition
| function is to designate proteins to the secretory pathway. it is a series of 7-12 hydrophobic amino acids |
|
|
Term
| what is the function of the nuclear pore? |
|
Definition
to allow proteins to get in and out of the nucleus (folded proteins)
there are nucleoporin proteins that extend into the nuclear pore, so it is not just a hole |
|
|
Term
| how does a protein get through the nuclear pore? |
|
Definition
by interacting with an importin protein and the nuclearporins, which allows the cargo to diffuse through the meshwork.
there are FG repeats on the nucleoporins and the importin has an affinity for FG repeats |
|
|
Term
| what is the role of Ran and the importins in getting a protein in through the nuclear pore? |
|
Definition
Importin is the protein that the cargo (other proteins) bind to in order to enter the nucleus
Ran is the GTP-binding protein that is high in the nucleus and low in the cytosol. Transport of a protein into the nucleus requires a Ran gradient (how you get directionality through the pore). The enzymes that activate (GEF) and deactivate (GAP) GTP via Ran are primarily located in the nucleus (GEF) and cytosol (GAP).
Ran-GTP binds to importins once they are in the nucleus, which causes them to release their cargo. This complex exits the nucleus. Ran will be activated on by Ran GAP, and dissociates from the importin. The Ran GDP will enter the nucleus thorugh a different mechanism so the whole process can restart.
RanGTP has a higher affinity for the importin than the cargo does, which occurs in the nucleus. Basically you are pulling the equilibrium to the side that the Ran GTP is on, because that's where the greater affinity for the importin is. |
|
|
Term
| how does the protein get out of the nucleus? |
|
Definition
| uses proteins called exportins that bind to the substrate AND Ran GTP |
|
|
Term
| How are NISs and NESs related? |
|
Definition
| One sequence can be activated and then another inactivated. This can switch when the protein is phosphorylated, which might turn one signal off and another on. |
|
|
Term
| what are the general features of the route a secreted or plasma membrane protein takes as it makes it way from the ribosome to the plasma membrane? |
|
Definition
-transcribed on a ribosome located on the ER membrane.
-protein ends up inside the ER
-vesicle buds off and fuses with the cis side of the golgi
-other modifications occur in golgi
-vesicle buds off from trans side of golgi and fuses with the membrane |
|
|
Term
| what is the basic mechanism of protein translocation into the ER? |
|
Definition
:crossing a membrane while being translated
-ribosome is recruited to the ER membrane by a SRP (signal recognition protein).
-the signal sequence binds to a protein in the membrane of the ER (makes sense because the signal sequence is hydrophobic)
-SRP releases when ribosome binds (via GTP hydrolysis)
-protein is translated from the ribosome into the ER
-once protein is translated, the signal sequence is cleaved off
**membrane proteins will end up bound in the membrane, wont' fully cross it |
|
|
Term
| how are membrane proteins inserted into the membrane during translation? |
|
Definition
|
|
Term
| how are membrane proteins inserted into the membrane during translation? |
|
Definition
| they exit the translocon via a lateral gate. the remaining polypeptide is translated into the cytosol, NOT the ER lumen. |
|
|
Term
| what is the difference between single pass and multi-pass protein insertion into the membrane? |
|
Definition
| the signal sequence, called the "signal anchor sequence" is not cleaved off for multi-pass proteins |
|
|
Term
| how are disulfide bonds formed in the ER? |
|
Definition
| disulfide bonds are formed by using reduced PDI, which has two sulfides attached to it. One of the sulfides attacks the H on the cysteine residue on the peptide. This creates S- which then attacks the other cysteine residue. The result is a bond, and the S's on the PDI are both reduced to SH |
|
|
Term
| what is the purpose of adding disulfide bonds to proteins? |
|
Definition
-stabilizes protein by helping reinforce protein's conformation
-can only form in the ER |
|
|
Term
| what is the role of N-glycosylation in protein folding and quality control? |
|
Definition
-adds a sugar to proteins.
-helps to fold proteins and protects them from degradation by proteases
-also used as a recognition signal
-many proteins that are secreted/end up in the cell matrix are glycosylated |
|
|
Term
| what is the residue that the N-glycosylation adds to? what is it usually surrounded by? |
|
Definition
Asn-X-Ser/Thr
added to Asn |
|
|
Term
| What is the name for the kind of glycosylation that is added on to the Asn residue? |
|
Definition
|
|
Term
| what is the name for the kind of glycosylation that happens in the Golgi? |
|
Definition
|
|
Term
| what is the role of glycosylation in protein folding and quality control? |
|
Definition
| Glycosylation helps protein fold. Initially the sugar on the protein contains a glucose. This glucose is eventually cleaved. At this point, if it is properly folded it will exit the ER. If the protein doesn't properly form, the glucose will be added back on or it will be marked for destruction. |
|
|
Term
| what is constitutive secretion? |
|
Definition
| it is the "default pathway" for proteins. They will go through the secretory pathway and either end up in the membrane or be exported from the cell |
|
|
Term
| what direction does vesicular transport occur in? |
|
Definition
| both directions. From ER to Golgi and from Golgi to ER (otherwise one would end up with no membrane...) |
|
|
Term
| How do proteins traffic from one part of the cell to another? |
|
Definition
| they have to have a signaling mechanism |
|
|
Term
| how does the ER retain/retrieve its proteins? |
|
Definition
| they have a KDEL sequence on them. There is a KDEL receptor in the Golgi that binds this sequence at a low pH and sends them back to the ER where they are released at a neutral pH |
|
|
Term
| how do proteins trafic from one vesicular compartment to another? |
|
Definition
-they use sorting signals (ex. lysosome and secretory granules)
ex. lysosomes have a mannose-6-phosphate attached to them and there is a receptor for the mannose in the TGN (trans golgi network) the receptor brings the protein to the lysosome, where the receptor dissociates from the protein due to the low pH |
|
|
Term
| what is regulative secretion? |
|
Definition
instead of following the default pathway, cells store a particular protein in a vesicle, however to release this protein the cells need an outside stimulus, ex. hormone or neurotransmitter. Allows the cell to release a lot of protein at one time
ex. insulin |
|
|
Term
| what are the three steps in vesicular transport? |
|
Definition
|
|
Term
| what is the function of coats in vesicular transport? |
|
Definition
coats are needed for budding
coats bind to the protein cargo and alter the shape of the membrane, ultimately pinching off the vesicle |
|
|
Term
| what are the kinds of coat proteins used in the ER, Golgi and plasma membrane? |
|
Definition
|
|
Term
| What is the mechanism that activates Sar1 |
|
Definition
inactive Sar1 GDP is activated by a GEF, SAR-1-GEF that exchanges GDP for GTP.
When GTP is bound, the amphipathic helix of Sar-1 sticks its hydrophobic side into the membrane which allows the inner and then outer layers of the COPII proteins to coat the membrane, the coat proteins also attach to the cytoplasmic tails of transmembrane proteins |
|
|
Term
| what is the role of SNAREs in vesicle fusion and targeting? |
|
Definition
there are two kinds of SNAREs: v and t (v for vesicle, t for target membrane)
the SNAREs pair together, a v and t, and pull each other together, eventually fusing the membranes |
|
|
Term
|
Definition
| an ATPase NSF disassembles the SNARE complexes |
|
|
Term
|
Definition
yes, basically each pathway in the cell has it's own SNAREs.
Only certain SNAREs result in fusion
ex. golgi to membrane has different snares than ER to golgi |
|
|
Term
| are the membranes of cells similar on the interior and exterior? |
|
Definition
no.
usually have an apical side and a basolateral side. cells are connected by tight junctions (ex. stomach cells, liver cells) |
|
|
Term
| what are the basic steps of endocytosis? |
|
Definition
-ligand binds to receptor in membrane
-coat proteins pinch off a vesicle from the membrane
-clathrin or other coat falls off
-Hydrogen atoms are pumped into vesicle
-receptors and ligands dissociate
-reeptors go to lysosome (ex. LDL cholesterol)
-receptors are recycled to plasma membrane |
|
|
Term
| how does protein trafficking regulate cholesterol biosynthesis? |
|
Definition
in LOW CHOLESTEROL situations:
-SREBP protein is attached to ER membrane
-moved to Golgi, part of protein in lumen is cleaved
-part of membrane protein is cleaved
-moves to nucleus to bind to SRE (sterol regulatory element) in 5' region of gene
-activates transcription--> melvonic acid
-meanwhile, HMG-CoA reductase has a phosphate that is removed, rendering it active
-it reduces the melvonic acid to cholesterol
cholesterol acts in a negative feedback mechanism to repress this whole chain of events once there is enough cholesterol in the cell. |
|
|
Term
| what was learned from the Anfinsen experiment? |
|
Definition
idea at the time was that a protein's ability to fold is hard wired into its AA sequence
however, in reality there are a lot of proteins in the cell that make it hard for other proteins to fold and can lead to issues like agglutination
basically he looked at his protein in a vacuum (no other proteins were present) so he avoided this issue altogether. |
|
|
Term
| what is the heat shock response? |
|
Definition
if cells are exposed to very high heat they won't survive; however if they are exposed to a modest heat exposure, they will survive a greater heat increase later.
heat shock response turns on a transcription factor that turns on the genes for heat shock proteins. induced by misfolded proteins |
|
|
Term
| what is the function of HSPs (heat shock proteins)? |
|
Definition
| most function to assist protein folding |
|
|
Term
| what is the general molecular function of chaperones? |
|
Definition
| to recognize misfolded proteins and help them fold properly (or direct them to a ubiquitin ligase) |
|
|
Term
| what are protein aggregates? where do they occur? |
|
Definition
| -they are globs of misfolded proteins that stick together because of hydrophobic residues that are on the outsides of the protein -they occur in the ER |
|
|
Term
| why is protein aggregation problematic to the cell? |
|
Definition
| because they can be toxic and the entry into the aggregate can be irreversible |
|
|
Term
| how do amyloid aggregates differ from other protein aggregates? |
|
Definition
formation is mediated by Beta sheet interactions, rather than simply through hydrophobic interactions.
amyloid is also very ordered compared to other aggregates |
|
|
Term
| how do chaperones prevent aggregation? |
|
Definition
| they bind to the protein before they aggregate and let them fold independently. |
|
|
Term
| What is the basic mechanism of GroE? |
|
Definition
| GroEL has hydrophobic residues on the inside of its protein. It binds to the protein and then binds another protein GroES, which also attaches via the hydrophobic residues. Once GroES binds, the area inside expands and the hydrophobic sites are withdrawn, so the protein can fold. ATP is used to help the protein change and expand. |
|
|
Term
| what is the basic mechanism of Hsp70? |
|
Definition
| rather than being encapsulated, the protein polypeptide is threaded through the Hsp70. it only traps a small, unfolded part of the protein and also uses ATP to drive the cycle of protein binding and release. J proteins deliver the substrate to the hsp70, which has its lid "open," then the ATP is used to shut the lid and the j protein dissociates. Once the protein has properly folded, ATP is used to open the lid again to release the protein |
|
|
Term
| what is the function of CHIP? |
|
Definition
to ubiquinate Hsp70 once there are no more misfolded proteins
to ubiquinate misfolded proteins inside Hsp70 |
|
|
Term
|
Definition
any condition where there is an overaccumulation of unfolded proteins which compromises the ERs ability to function as a site for protein folding and modification.
ex. glucose and Ca2+ can affect ER stress |
|
|
Term
| what is the UPR response? |
|
Definition
unfolded protein response
reaction to ER stress
-intensify synthesis of chaperones
-intensify synthesis of protein degradation machinery
-suppress protein synthesis
-extreme situations, cell death pathways are activated |
|
|
Term
| what is the ERAD pathway? |
|
Definition
ER-associated degradation
misfolded proteins in the ER lumen are signalled to be sent to the cytosol where they are degraded by the ubiquitin pathway |
|
|
Term
| how does the cell inhibit protein synthesis in response to ER stress? |
|
Definition
|
|
Term
|
Definition
| need iron to carry out many important functions in our bodies: binding O2 in the blood, DNA synthesis, drug detox |
|
|
Term
| why is too much iron problematic? |
|
Definition
| because it can lead to organ toxicity, DNA damage and hemachormatosis |
|
|
Term
| what are the functions of transferrin? |
|
Definition
-extracellular
-has a very high affinity for iron
-transports it through circulation and delivers it to cells by binding transferrin receptors |
|
|
Term
| what are the functions of ferritin? |
|
Definition
-binds to iron within cells
-contains up to 4500 iron atoms withiin central core as rust
-has oxido-reductase activity allows iron to be converted to a soluble form when needed |
|
|
Term
| why are iron binding proteins important? |
|
Definition
| to keep it away from other molecules that it could damage and to solubize it in a way that makes it available |
|
|
Term
| what is the function of DMT1? |
|
Definition
to transport iron into the enterocytes
first Fe3+ has to be reduced to Fe2+
DMT1 is a symporter, transports Fe2+ and H+ down its concentration gradient |
|
|
Term
| what is the function of ferroportin? |
|
Definition
to move iron out of the enterocyte across the basolateral membrane
Fe2+ needs to be converted back to Fe3+ so that it can bind to transferrin and be distributed to the peripheral tissues |
|
|
Term
| why are iron transporters necessary? |
|
Definition
| -because Iron Fe3+ cannot cross the membranes |
|
|
Term
| what happens to DMT1 and FPN1 in an iron depleted state? |
|
Definition
| DMT1 is upregulated by 1) increased synthesis of the protein, 2) DMT1 mRNA is more stable FPN1 is expressed over a greater surface (protein stability is increased) (so there is less iron in the villus, which indicates more transport) |
|
|
Term
| what happens to DMT1 and FPN1 in an iront replete state? |
|
Definition
| Hepcidin blocks iron transport into enterocytes and out of them. is high in iron overload. |
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Term
| how does hepcidin regulate iron homeostasis? |
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Definition
| it regulates the amount of FPN1 receptors on the basolateral membrane by phosphoryllating an intracellular loop which promotes endocytosis |
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Term
| how is transferrin taken up by erythroid cells? |
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Definition
| 1) transferrin bound to two irons binds to receptor proteins on erythrocytes, they bind in at clathrin coated pits. |
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Term
| how is iron released from transferrin and incorporated into hemoglobin? |
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Definition
2) the endosome is acidified, which promotes release of iron from transferrin
3) the transferrin is reduced from Fe3+ to Fe2+ and transported by DMT1 into the cytosol
4) the iron is transported into the mitochondria where it is formed into heme |
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