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173 Cards in this Set
- Front
- Back
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What level of gene regulation changes chromosome structure or number?
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chromosomal
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What level of gene regulation changes the rate of mRNA synthesis?
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transcriptional
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What level of gene regulation changes mRNA maturation, localization, or stability?
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post-transcriptional
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What level of gene regulation changes the rate of protein synthesis?
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translational
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What level of gene regulation changes protein modification, sorting, complex formation, or stability?
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post-translational
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What is the term for addition or deletion of entire sets of chromosomes?
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polyploidy
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What is polyploidy?
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addition or deletion of entire sets of chromosomes
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What is the term for addition or deletion of individual chromosomes within a set?
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aneuploidy
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What is aneuploidy?
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addition of deletion of individual chromosomes
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What happens in a translocation?
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parts of two chromosomes split and swap with each other
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What type of chromosomal change involves parts of two chromosomes splitting and swapping with each other?
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translocation
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What happens in an inversion?
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parts of one chromosome split and rejoin incorrectly
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What type of chromosomal change involves parts of one chromosome splitting and rejoining incorrectly?
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inversion
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What is a ring chromosome?
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chromosome breaks and rejoins as a ring
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What is an isochromosome?
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chromosome containing two of the same pieces
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What type of chromosomal change results in one chromosome containing two of the same pieces?
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isochromosome
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What type of chromosomal change involves the loss of a chromosome?
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deletion
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What are the types of local numerical changes at the chromosomal level?
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gene amplification
gene deletion |
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What are the types of local structural changes at the chromosomal level?
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gene inversion
missense mutation nonsense mutation frameshift |
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What is the significance of the promoter region?
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site where RNA polymerase binds to initiate transcription
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Are activator and operator sites known as cis-acting or trans-acting elements?
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cis-acting
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Are activators and repressors known as cis-acting or trans-acting elements?
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trans-acting
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Are cis-acting elements the activators and repressors or the activator and operator sites?
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activator and operator sites
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Are trans-acting elements the activators and repressors or the activator and operator sites?
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activators and repressors
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Which three genes in the lac operon code for the enzymes that metabolize lactose?
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thiogalactoside transacetylase (A)
galactose permease gene (Y) beta galactosidase (Z) |
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What is the sequence of genes in the lac operon?
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P(I) - I - A' - P(ZYA) - O - Z - Y - A
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What is the effect of I repressor protein on the lac operon?
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binds to the operator region to block RNA polymerase from binding to the promoter
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How is I repressor protein inactivated?
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when lactose concentration is high, some leaks into the cell, becomes allolactose, and binds to I repressor protein to prevent it from binding to the operon
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Is the lac operon activator protein made in an active or inactive form?
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inactive
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Is the lac operon I repressor protein made in an active or inactive form?
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active
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What happens to the lac operon when lactose and glucose concentrations are high?
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basal transcription
I repressor inactive and CAP activator inactive |
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What happens to the lac operon when lactose and glucose concentrations are low?
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reduced or no transcription
I repressor active and CAP activator active |
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What happens to the lac operon when lactose concentration is low and glucose concentration is high?
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reduced or no transcription
I repressor active and CAP activator inactive |
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What happens when lactose concentration is high and glucose concentration is low?
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strong transcription
I repressor inactive and CAP activator active |
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How does the lac operon activator gene become activated?
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binds to cAMP to form an active DNA-binding protein complex
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Is tryptophan an essential amino acid?
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yes
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What happens to the Trp operon when tryptophan concentration is low?
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RNA polymerase binds to the promoter to allow production of enzymes that synthesize tryptophan
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What happens to the Trp operon when tryptophan concentration is high?
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Tryptophan binds to a repressor protein and this complex binds to the operator region to block RNA polymerase from binding to the promoter
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Is the Trp operon repressor protein made in an active or inactive form?
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inactive
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How long is the leader sequence for the attenuation mechanism of the Trp operon and where is it located?
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162 bp at the 5' end of mRNA
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What does the attenutation mechanism do for the Trp operon when tryptophan concentration is high?
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stem loop forms between S2 and S3 domains, and transcription and translation continue
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What does the attenutation mechanism do for the Trp opeon when tryptophan concentration is low?
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stem loop forms between S3 and S4 domains, and transcription fails to complete (pseudo-transcription stop signal)
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What does the leader sequence for the attenuation mechanism of the Trp operon contain?
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start codon, S1, S2, S3, S4 domains
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How long is the leader sequence for the attenuation mechanism of the Trp operon and where is it located?
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162 bp at the 5' end of mRNA
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What does the leader sequence for the attenuation mechanism of the Trp operon contain?
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start codon, S1, S2, S3, S4 domains
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What is the purpose of an insulator?
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prevents an enhancer from inappropriately binding to and activating the promoter of another gene in the same region of the chromosome
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What is the name for stretches of DNA (>42 bp) between enhancers and promoters/silencers of adjacent genes or clusters of adjacent genes?
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insulators
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What is an example of an insulator?
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between alpha and delta gene promoters of T-cell receptors
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What are the three steps involved in mRNA processing?
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5' capping
3' polyadenylation splicing out introns |
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CGRP results from alternative splicing of what gene?
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rat calcitonin gene
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What results from alternative splicing of rat calcitonin gene?
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CGRP
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What is the purpose of untranslated 5' and 3' regions of mRNA?
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provide stability by protecting transcripts from nuclease attack
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What are the proteins that are made by apoprotein B located?
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liver and intestine (half the size)
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What is the function of liver Apo-B?
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delivers cholesterol to body tissues by binding LDL receptors
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How is ingested iron brought into cells?
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it's carried through the circulation bound to transferrin protein, and this complex is brought into cells by interacting with transferrin receptor in the plasma membrane
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What structual feature does transferrin receptor mRNA have and what is its importance?
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hairpin loops in 3' untranslated region that signal RNase for mRNA degradation when active
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When iron stores are sufficient, does IRE-BP bind to the hairpin loop structures of transferrin receptor mRNA?
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no, so there is increased degradation of transferrin receptor mRNA that already exists inside the cells
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When iron stores are insufficient, does IRE-BP bind to the hairpin loop structures of transferrin receptor mRNA?
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yes, so there is rapid synthesis and accumulation of receptor protein
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Does siRNA originate from single-stranded or double-stranded DNA?
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double-stranded
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Does miRNA originate from single-stranded or double-stranded DNA?
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single-stranded
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Is siRNA often 100% complementary to its target?
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yes
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Is miRNA often 100% complementary to its target?
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no
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What protein breaks DNA down to 20-30 bp pieces?
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dicer
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What is the function of dicer?
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breaks DNA down to 20-30 bp pieces
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What is the function of RISC?
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RNase activity to degrade the target of siRNA-protein complex
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What is affected by trans-factor regulation of translation?
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eIF2 and eIF4E
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What's the difference in the location of cis-acting elements in prokaryotes and eukaryotes?
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prokaryotes: nearby or overlapping with the RNA binding site
eukaryotes: not restricted to promoter region (can be found in introns, exons, and 3' downstream sequences) |
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What is unique about a polycistronic mRNA?
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it contains multiple sets of translation start and stop codons, so numerous different proteins can be produced from a single transcript
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Is eIF2 active or inactive when it is phosphorylated by kinase?
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inactive
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What inactivates kinase?
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binding with heme
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Is eIF4E active or inactive when it is bound to 4E-BP1?
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inactive
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How does eIF4E become active?
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4E-BP1 must be phosphorylated and released from the eIF4E
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How does eIF4E lead to initiation of translation?
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binds to 5' cap of mRNA, secondary structure is unwound, 48S forms, scanning for AUG start codon, release of initiation factors, 80S formation
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What is the Kozak consensus sequence?
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gccgcc(A/G)ccAUGG
eukaryotic equivilent of Shine-Delgarno sequence (translational start site) |
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What does the internal ribosome entry sequence (IRES) allow for?
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allows translation initiation in the middle of a mRNA sequence
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How does the internal ribosome entry sequence (IRES) work?
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IRES mimics 5' cap structure and is recognized by 40S pre-initiation complex
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What kind of proteins are synthesized through the IRES mechanism?
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proteins associated with differentiation (not actively proliferating)
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What is iron responsive element (IRE)?
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hairpin loop in 5' region that is bound by IRE-BP when iron level is low
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What happens to ferritin when iron level is low?
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IRE-BP binds to IRE, which prevents read-through processoff ribosome complex
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What happens to ferritin when iron levels are high?
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IRE-BP cannot bind to IRE, so ferritin mRNA can be translated efficiently
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What are the characteristic features of the nuclear localization signals that target proteins to the nucleus?
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contain several consecutive or closely spaced charged residues
can be located in any region of the protein not removed after protein is transported into the nucleus |
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What are the unique characteristics of the matrix targeting sequences (MTS) that target proteins to mitochondria?
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15-35 amino acids long
enriched in positively charged residues located at the N-termini removed from mature proteins |
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What are the names of the chaperon proteins that keep proteins unfolded as they are brought to the outer mitochondrial membrane?
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hsp70 and MSF
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What is the name of the first receptor protein that interacts with unfolded proteins targeted for the mitochondria?
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Tom 20/22
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What is the name of the channel in the outer mitochondrial membrane that unfolded proteins pass through?
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Tom 40
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What is the name of the channel in the inner mitochondrial membrane that unfolded proteins pass through?
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Tim/23/17
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What protein binds to an unfolded protein to pull it into the mitochondrial matrix?
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hsp70
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What two important enzymes do peroxisomes contain?
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oxidases generate hydrogen peroxide
catalases degrade peroxide to water and oxygen |
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What is the targeting signal for peroxisome proteins?
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SKL (serine-lysine-leucine) located at the C-termini
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How are peroxisome proteins transported?
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iron-containing tetramers that are kept unfolded by the iron-heme group
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How do peroxisome proteins get into the peroxisome lumen?
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PTSIR complexes with the protein through SKL, which opens channel protein Pex140
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What happens to chaperon protein PTSIR after a peroxisome protein enters the peroxisome lumen?
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it dissociates from the tetramer and recycles back to the cytosol
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Is the SKL targeting signal cleaved after a peroxisome protein reaches its destination?
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no
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What kinds of groups can be attached to a soulble cytosolic protein in order to anchor it to a membrane?
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fatty acyl or prenyl
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Where does myristoylation occur?
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N-terminus glycine
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Where does farnesylation occur?
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C-terminus cysteine, specifically targeting C-a-a-X
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Where does palmitoylation occur?
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internal cycteine residues
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Where does geranylgeranylation occur?
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C-terminus cysteine, specifically targeting C-C, C-X-C, or C-C-X-X
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True or False: All nuclear encoded proteins are initially synthesized on free ribosomes.
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True
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What determines what classes of proteins are synthesized by a ribosome?
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ER signal peptide sequence
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Which end of a protein is the ER signal peptide sequence typically located at?
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N-terminus
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What does an ER signal peptide sequence typically consist of?
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one or more charged amino acids followed by 6-12 hydrophobic residues
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What is the first step in protein synthesis by ER-bound ribosomes?
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mRNA is translated by a free ribosome in the cytosol
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What is the second step in protein synthesis by ER-bound ribosomes?
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ER signal peptide sequence binds signal recognition particle (SRP) to block translation
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What is the third step in protein synthesis by ER-bound ribosomes?
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mRNA-SRP-SRP receptor complex brings ribosome to outer ER membrane
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What is the fourth step in protein synthesis by ER-bound ribosomes?
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binding of ribosome to translocon opens the channel and promotes dissociation or SRP from ER-signal sequence, allowing translation to continue in ER lumen
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What is the fifth step in protein synthesis by ER-bound ribosomes?
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ER signal peptide is cleaved by signal peptidase
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What is the sixth step in protein synthesis by ER-bound ribosomes?
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once protein synthesis is complete, ribosome released from translocon and is recycled
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What are the four principle checkpoints that newly synthesized polypeptides in the ER undergo before they can reach their final destinations?
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disulfide bond formation
protein folding glycosylation assembly into multimeric proteins |
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Which checkpoint modifications apply to all proteins made from ER-ribosomes?
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protein folding
glycosylation |
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What checkpoint modifications take place exclusively in the ER (not in the ER and golgi)?
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disulfide bond formation
protein folding assembly into multimeric proteins |
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What happens to the unfolded and misfolded proteins that aren't allowed to be transported from ER to golgi?
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move back to cytosol through translocon channel where they are targeted for degradation by ubiquitin-dependent 26S proteosome
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Where is O-linked glycosylation carried out?
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golgi
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Where is the sugar unit attached to the protein in O-linked glycosylation?
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hydroxyl group of serine or threonine
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How is the sugar unit added to the protein in O-linked glycosylation?
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one at a time, each catalyzed by a different glycosyltransferase enzyme
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What is the structure usually like for O-linked glycosylation?
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very short, containing 1-4 sugar units
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Where is N-linked glycosylation carried out?
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endoplasmic reticulum and golgi
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Where is the sugar unit attached to the protein in N-linked glycosylation?
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amide group of asparagine
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How is the sugar unit added to the protein in N-linked glycosylation?
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begins with addition of large preformed oligosaccharide, then others are added or removed one at a time
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What is the structure usually like for N-linked glycosylation?
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branchy and complex, containing more than 10-15 sugar units
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What does the common preformed oligosaccharide for N-linked glycosylation consist of?
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2 GlcNac
9 mannose 3 glucose |
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What is the N-linked precursor oligosaccharide built upon?
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pyrophosphoryl residue of dolichol (75-95 C long)
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Is the final dolichol-pyrophosphoryl oligosaccharide oriented towards the inside or outside of the ER?
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inside
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Do the majority of glycoproteins have O-linked or N-linked glycosylation?
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O-linked
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What is the name for proteins whose synthesis is complete by ER-ribosomes?
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glycoproteins
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About how many hydrolytic enzymes to lysosomes contain?
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60-70
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What signal targets lysosomal proteins to lysosomes?
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mannose-6-phosphate
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How is mannose-6-phosphate added to lysosomal proteins?
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Phosphotransferase adds a phospho-N-acetyl glucosamine unit from UDP-GlcNac to the hydroxyl group of mannose, and a phosphodiesterase removes the glucosamine.
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What do the intrinsic signal sequences in lysosomal proteins recognize and what is their purpose?
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GlcNac phosphotransferase
prevents non-lysosomal glycoproteins from acquiring phosphate in their mannose residues |
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What is clathrin made up of, and what kind of structure does it form?
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3 heavy chains and 3 light chains
forms closed polyhedral structure |
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What is the first step in lysosomal protein sorting?
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mannose-6-phosphate residues of the protein bind to receptors in the trans-golgi complex
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What is the second step in lysosomal protein sorting?
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vesicles containing protein-receptor complex bud via clathrin-dependent mechanism
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What is the third step in lysosomal protein sorting?
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vesicles fuse with late endosomes (pH = 5.5)
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What is the fourth step in lysosomal protein sorting?
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lysosomal protein dissociates from mannose-6-phosphate receptor within late endosomes
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What is the fifth step in lysosomal protein sorting?
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phosphatase removes phosphate group from mannose, which prevents it from rebinding to the receptor
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What is the sixth step in lysosomal protein sorting?
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late endosomes split into two types of transport vesicles
1. delivers lysosomal proteins to lysosomes 2. recycles unbound receptors by fusing with trans-golgi or plasma membrane |
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What is the transport of transmembrane and secretory proteins from the golgi to cell membrane dependent on?
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GTP-GDP
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How is regulated transport different from consecutive transport?
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regulated stores the protein inside the cell until there is a stimulus
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What does the transmembrane and secretory protein sorting signal consist of?
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highly hydrophobic amino acids
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True or False: Sorting signal is unique to proteins made by ER-bound ribosomes.
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False
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What does the ER retention signal consist of and where is it located in ER proteins?
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KDEL (lysine-aspartic acid-glutamic acid-leucine) at the C-terminal end
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How does the ER retention signal work?
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binds to KDEL-specific membrane receptors in cis-golgi, and these complexes are transported in vesicles back to the ER
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True or False: KDEL receptors are recycled once the ER protein is brought back to the ER.
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True
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Which protein groups require a minimum of 0 types of cis elements for sorting?
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cytosolic
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Which protein groups require a minimum of 1 type of cis elements for sorting?
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nuclear
mitochondrial peroxisome membrane-associated cell surface and secreted |
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Which protein groups require a minimum of 2 types of cis elements for sorting?
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endoplasmic reticulum
membrane lysosomal |
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What are the typical chemical modifications that affect proteins?
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hydroxylation
acetylation methylation carboxylation ADP ribosylation phosphorylation fatty acylation glycosylation |
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Which chemical modification of proteins involves addition to lysine and proline?
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hydroxylation
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Which chemical modification of proteins involves addition to the N-terminal group?
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acetylation
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Which chemical modification of proteins involves addition to histidine?
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methylation
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Which chemical modification of proteins involves addition to glutamine?
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carboxylation
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Which chemical modification of proteins involves addition to threonine and tyrosine?
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phosphorylation
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Which chemical modification of proteins involves addition to arginine?
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ADP ribosylation
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Which chemical modification of proteins is common in extracellular matrix proteins such as collagen?
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hydroxylation
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Which chemical modification of proteins plays an important role in controlling the life span of proteins within cells?
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acetylation
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Which chemical modification of proteins is common in prothrombin?
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carboxylation
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Which chemical modification of proteins is common in actin and regulates cell cycle proteins in differentiation of CNS neuronal cells?
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methylation
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Which chemical modification of proteins is common in bacterial toxins?
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ADP-ribosylation
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Which chemical modification of proteins is the most common chemical alteration used in regulating protein activity?
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phosphorylation
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What does hydroxylation involve and where is it commonly found?
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addition of OH to lysine and proline
common in extracellular matrix proteins such as collagen |
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What does acetylation involve and where is it commonly found?
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addition of CH3CO to N-terminal amino group of a protein
plays important role in controlling lifespan of proteins within cells |
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What does methylation involve and where is it commonly found?
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addition of CH3 to histidine
common in actin and regulates cell cycle proteins involved in differentiation of CNS neuronal cells |
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What does carboxylation involve and where is it commonly found?
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addition of COOH to glutamine
common in prothrombin |
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What does ADP-ribosylation involve and where is it commonly found?
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addition of ADP-ribose from NAD+ to arginine
common in bacterial toxins |
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What is involved in phosphorylation and where is it commonly found?
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addition of phosphate group to serine, threonine, and tyrosine
most common chemical alteration used in regulating protein activity |
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What are the three enzymes involved in ubiquitin-mediated protein degradation?
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E1 - ubiquitin activating enzyme
E2 - ubiquitin conjugating enzyme E3 - ubiquitin protein ligase |
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What component complexes make up the 26S proteosome?
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20S (catalytic) and 2 19S complexes
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What makes insulin a prepropolypeptide?
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ER-recognition signal
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What is the structure of mature insulin?
|
two separate polypeptide chains held together by intra- and inter-chain disulfide bonds
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How is the insulin propolypeptide activated?
|
removal of a C-peptide by an intracellular protease
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Are genes that contain more 5-methylcytosine less readily or more readily transcribed than those that are unmethylated?
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less readily
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What does the attenutation mechanism do for the Trp operon when tryptophan concentration is high?
|
stem loop forms between S3 and S4 domains, and transcription fails to complete (pseudo-transcription stop signal)
|
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What does the attenutation mechanism do for the Trp opeon when tryptophan concentration is low?
|
stem loop forms between S2 and S3 domains, and transcription and translation continue
|
