Module 4 Sections 4-7 Flashcards

Question

GTP

Answer 1

energy currency of translation

Answer 2

associates with the small subunit to prevent the premature assembly of the ribosome

Answer 3

guides the charged initiator tRNA with the AUG start codon in the P site

Answer 4

blocks the A site to ensure the correct alignment of the tRNA with the AUG start codon

Answer 5

guides the initiating 5'-AUG to its correct position Signal of 4-9 purine residues, situated 8-13 nucleotides on the 5' side of the start codon The sequence base pairs with a complementary pyrimidine-rich sequence near the 3' end of the 16S rRNA of the small ribosomal subunit which positions the 5'-AUG sequence of the mRNA in the precise location on the 30S subunit, where it is required for translation initiation

Answer 6

The amino acid incorporated in response to the 5'-AUG initiation codon Formed by methionine attaching to tRNA(fMet) by the Met-tRNA synthetase, and also a transformylase enzyme transferring a formyl group to the amino group of the methionyl part of the tRNA Addition of the formyl group = fMet residue cannot be added internally (the N group is blocked)

Answer 7

Used to bring in methionine residue when there is an AUG codon within the mRNA transcription (not at the 5' initiation position) The absence of the N-formyl group enables it to insert a methionine residue at internal positions within the growing polypeptide chain

Answer 8

tRNA fMet is charged with N-formylmethionine and this amino acid is incorporated in response to the 5-AUG initiation codon tRNA Met is charged with the amino acid methionine and inserts the Met residue internally within the polypeptide chain

Answer 9

a contiguous mRNA with more than 2 genes that can be translated into proteins

Answer 10

bacterial = poly eukaryotic = mono

Answer 11

encodes for a single protein

Answer 12

overlapping or non-overlapping

Answer 13

The open reading frame for each gene is distinct from one another and they will have separate Shine-Dalgarno sequences

Answer 14

Despite lacking a Shine-Dalgarno sequence for each internal start site, the internal open reading frames can be translated efficiently because of overlapping start and stop codons, usually 5'-AUGA Ribosomes terminating translation of the upstream message can initiate the downstream message simply by shifting their reading frame Overlapping genes Shine-Dalgarno sequence Protein-coding region I Protein-coding region 2

Answer 15

sequence around the start codon in eukaryotic mRNA that guides translation - has a purine nucleotide 3 residues before, and a G residue immediately after the start codon

Answer 16

surrounds the initiation site

Answer 17

enhance translation through contact with the eukaryotic initatior tRNA through its anticodon arm

Answer 18

a single mRNA transcript bound by multiple ribosomes

Answer 19

subunits of the eukaryotic initiation factor interacts with either the 5' cap or poly(A) binding protein (PABP) which is associated with the 3' poly(A) tail of the mRNA molecule

Answer 20

poly(A) binding protein

Answer 21

Ensuring that mRNA processing is complete prior to translation Promoting translational efficiency Enabling the sophisticated translational regulation of gene expression

Answer 22

The nascent polypeptide is lengthened by the covalent attachment of successive amino acid units Each unit is carried to the ribosome and correctly positioned by its tRNA which base pairs to its corresponding codon in the mRNA Energy currency – GTP (guanosine triphosphate) and not ATP Dipeptidyl-tRNA = a tRNA carrying a growing peptide chain of 2 peptides

Answer 23

1. binding of an aminoacyl-tRNA in the A site 2. peptide bond formation between the polypeptide in the P site and the amino acid in the A site, transferring the growing polypeptide chain to the tRNA in the A site

Answer 24

delivers a charged tRNA to the A site of an active ribosome at the decoding center of the ribosomal complex

Answer 25

the energy is provided by the hydrolysis of EF-Tu-GTP to EF-Tu-GDP + Pi

Answer 26

occurs when the correct codon base pairs with an anticodon and the ribosome changes configuration

Answer 27

gets dissociated

Answer 28

release of EF-Tu-GDP

Answer 29

EF-Tu-GDP is recycled to EF-Tu-GTP through the actions of the EF-Ts: the guanine nucleotide exchange factor for EF-Tu

Answer 30

guanine nucleotide exchange factor for EF-Tu

Answer 31

2 adenosine residues (A1492 and A1493) "flip out" in response to correct codon-anticodon base pairing

Answer 32

1. tRNAs are delivered to the A-site by GTP-bound EF-Tu 2. A1492 and A1493 of the ribosomal A-site "flip out" in response to correct codon-anticodon base pairing charged 3. EF-Tu-GTP is hydrolyzed to EF-Tu-GDP + Pi 4. tRNA rotates into position - accommodation

Answer 33

a peptide bond is formed between the 2 amino acids bound by their tRNAs to the A and P sites on the ribosome

Answer 34

1. Formation of the first peptide bond occurs through the transfer of the initiating N-formyl methionyl group from its tRNA in the P site to the amino group of the second amino acid on its tRNA in the A site 2. A nucleophilic attack of the alpha-amino group of the A-site aminoacyl-tRNA on the carbonyl carbon of the ester bond linking the fMet (or the growing peptide chain) to the P-site tRNA forms the peptide bond 3. The growing chain is transferred to the tRNA in the A site - As the ribosome shifts along the mRNA, the uncharged tRNA now moves to the E site and the peptidyl-tRNA moves to the P site - This frees the A site to bind the next tRNA

Answer 35

produced by bacteria/other microorganisms to inhibit protein synthesis in other bacteria

Answer 36

1. aminoglycosides 2. puromycin (aminonucleosides)

Answer 37

reduce translational accuracy - Binds specifically to the decoding center of the small ribosomal subunit and causes inappropriate flipping A1492/1493 even when an incorrect tRNA is positioned in the A site Kill bacteria through errors in translational fidelity by causing misfolded proteins and eventually cell death

Answer 38

gentamicin, streptomycin and paromomycine

Answer 39

mimics aminoacyl tRNA structure and prematurely stops protein synthesis

Answer 40

similar to the 3' end of an aminoacyl-tRNA so it can bind to the reibosomal A site and participate in peptide bond formation Since it only resembles the 3' end of the tRNA, it cannot engage in translocation and dissociates from the ribosome shortly after it is linked the C-terminus of the peptide

Answer 41

aminonucleosides: binds to the ribosomal A site and participates in peptide bond formation, but does not engage in translocation, stopping protein synthesis aminoglycosides: binds the small subunit (like EF-Tu) and causes inappropriate flipping of A1492/1493

Answer 42

release factors (RF)

Answer 43

RF-1 and RF-2

Answer 44

Recognize termination codons and bind the A-site of the ribosome in much the same way as tRNAs RF-1 recognizes stop codons UAG and UAA Rf-2 recognizes UGA and UAA Either one binds at the stop codon and induces peptidyl transferase to transfer the growing polypeptide to a water molecule rather than to another amino acid

Answer 45

transcriptional regulation

Answer 46

Haploid, so the effects of gene mutations are unmasked Easy to see the impact of a single mutated gene on bacterial function Need to initially understand gene regulation in simpler organisms to create networks of greater magnitude in other organisms

Answer 47

unit of genetic expression consisting of 1 or more cotranscribed genes and the operator and promoter sequences that regulate their transcription

Answer 48

1. A set of genes (A, B, and C) transcribed as a single mRNA 2. Adjacent regulatory regions that coordinately control the expression of the operon genes - Can contain the same promoter, activator, and repressor regions as genes

Answer 49

Polycistronic mRNA, containing 2 regulatory regions (lacl, lacO) and 3 genes that are referred to as the lac genes (lacZ, lacY, and lacA)

Answer 50

When lactose is available, the lac operon is turned on by the regulatory regions, and the 3 lac genes are expressed. When unavailable, transcription from the lac operon is greatly reduced

Answer 51

Encodes the lac repressor protein, which interacts with lacO to regulate transcription Repressor is transribed separately from the rest of the operon (has a separate promoter) and is always on

Answer 52

Lac operator Does not code for a gene product, but instead interacts with lacI to regulate transcription

Answer 53

Codes for the protein B-galactosidase, which catalyzes cleavage of lactose into its components, glucose and galactose that can be further metabolized to generate ATP

Answer 54

lactose to allolactose

Answer 55

B-galactosidase

Answer 56

Codes for the galactoside permease protein, which inserts into the bacterial plasma membrane and imports lactose into the cell

Answer 57

Codes for the protein thiogalactoside transacetylase, which modifies toxic galactosides that are imported along with lactose, facilitating their removal from the cell

Answer 58

protein that modifies toxic galactosides that are imported along with lactose, facilitating their removal from the cell

Answer 59

Phenomenon by which DNA is transferred from a donor to a recipient cell. The transfer is mediated by a genetic element, separate from the bacterial chromosome, known as the F plasmid)

Answer 60

mediates the transfer of DNA from a donor to a recipient cell

Answer 61

partially diploid bacterium which has its own chromosome complement and a chromosome fragment introduced by a process such as conjugation

Answer 62

using lac operon mutant e.coli to understand the mechanisms of gene regulation

Answer 63

Hypothesized that the lacl locus produced a diffusible product that could act on any DNA molecule, not just from the DNA which it was generated

Answer 64

examining the role of the lac operator

Answer 65

The lacO did not produce a diffusible substance The lac operon DNA from the lacO mutant could not be correctly regulated even in the presence of a wild-type copy of lacO LacI functioned like a transmitter If knocked out, it could be replaced by a second transmitter LacO functioned like a receiver If a message could not be received, the action (transcription of the lac genes) could not be controlled

Answer 66

examining the role of the lac operator part 2

Answer 67

Confirmed that the lacI gene encodes a diffusible molecule (acts in trans) that represses lac gene expression, whereas lacO controls only the expression of lac operon genes to which it is connected (acts in cis)

Answer 68

encodes a diffusible molecule

Answer 69

controls only the expression of lac operon genes to which it is connected

Answer 70

binding of a repressor protein that prevents or decreases expression ex: the binding of the lac repressor to the lac operator

Answer 71

required in order to block gene transcription

Answer 72

in the absence of lactose, which means that the bacteria is not wasting energy to produce the protein products of the lac operon required for lactose metabolism when there is no lactose present to metabolize

Answer 73

Homotetrameric DNA binding protein 2 dimers bound together at the end opposite to the DNA binding region Binding region contains a helix-turn-helix motif at the N-terminus, allowing it to bind to the major groove of DNA

Answer 74

4 identical subunits in a protein

Answer 75

1. 3' of promoter region 2. in lacZ gene 3. 5' of promoter

Answer 76

a single stranded sequence of nucleotides followed downstream by its reverse complement

Answer 77

repression via the lac repressor is not 100% effective

Answer 78

1. leaky expression 2. Binding of the repressor reduces the rate of transcription initiation by a factor of 1000, but even in the repressed state, each cell has a few molecules of B-galactosidase and galactoside permease, presumably synthesized on the rare occasions when the repressor transiently dissociates from the operators 3. When cells are provided with lactose, the few existing molecules of galactoside permease enable lactose from the medium to enter the cell

Answer 79

function as effectors under circumstances where activation of operon is needed

Answer 80

effector = a molecular signal that regulates the binding of a repressor to DNA (like allolactose)

Answer 81

A small molecule or protein binds the repressor and causes a conformational change that results in an increase or decrease in transcription

Answer 82

The effector binds to the repressor and induces a conformational change that results in dissociation of the repressor from its binding site on the DNA, allowing transcription to proceed

Answer 83

the interaction of an inactivating repressor and an effector molecule causes the repressor to bind to DNA, shutting down transcription

Answer 84

an allosteric effector

Answer 85

Induces the lac operon by binding to a specific site on the lac repressor, causing a conformational change that results in dissociation of the repressor from the operator

Answer 86

In the presence of glucose, the operon is blocked by catabolite repression, a form of positive regulation

Answer 87

the inhibition of the expression of genes required for the metabolism of, in the case of the lac operon, other sugars in the presence of glucose

Answer 88

activator protein that regulates positive regulation of the lac operon

Answer 89

Transcription is weak without an activator interacting with RNA polymerase to enhance DNA binding and transcriptional initiation

Answer 90

yes, each subunit binds 1 molecule of cAMP, which is required for binding of CRP to the activator binding site of the lac operon DNA

Answer 91

by an enzyme called adenylyl cyclase (ATP ---> cAMP + pyrophosphate)

Answer 92

Effectors in positive regulation bind an activator, rather than a repressor, to cause a conformational change that results in an increase or decrease in transcription

Answer 93

cAMP is required for binding of the activator (CRP) to the activator binding region of DNA, increasing expression

Answer 94

binding of the effector reduces the affinity of the activator for DNA, and inhibits expression

Answer 95

In the presence of glucose, cAMP production is decreased & cAMP is exported from the cell In the absence of glucose, cAMP production is increased and cAMP is retained in the cell

Answer 96

lactose availability causes repressor to dissociate low cAMP levels prevent CRP binding, meaning RNA polymerase may only occasionally initiate transcription

Answer 97

cAMP is low and the cAMP-CRP does not bind the operon. the repressor binds the operator, blocking RNA polymerase and preventing transcription of the lac genes

Answer 98

when glucose is absent and lactose is present, the activator binds a different small molecule, which causes it to bind DNA and recruit RNA polymerase for high-level gene expression

Answer 99

reqjired at all times, expressed at a constant level

Answer 100

Undergo activation and repression to changes in environmental conditions Require the assistance of transcription factors, and the proteins that alter the affinity of the RNA polymerase for the promoter Enhance gene expression = activators Reduce expression = repressors Regulators act by binding to specific DNA sequences known as regulatory sites, and either facilitating or inhibiting transcription

Answer 101

binding of a common transcriptional activator

Answer 102

from scratch by expression of its gene or an existing activator protein may become active for DNA binding through interaction with another protein or a small effector molecule

Answer 103

Removal of a common repressor bound to DNA sites, either by an allosteric change induced by binding of a small effector molecule, or by proteolytic digestion of the repressor

Answer 104

change in shape/conformation of binding site

Answer 105

Activator binds to a DNA binding region distant from the promoter, and the DNA is able to fold over so that it can make contact with the transcriptional machinery

Answer 106

Proteins that can make protein-protein interactions to influence transcription - don't bind to DNA directly, just other proteins

Answer 107

Act as a bridge between an activator and the RNA polymerase to activate transcription

Answer 108

Act as a block to inhibit binding of the activator to the RNA polymerase and prevent transcription

Answer 109

have methods to regulate groups of genes simultaneously: both often have several activator and repressor binding sites per gene: eukaryotes have polycistronic genes: bacteria use distant regulatory sites that act through DNA loops: eukaryotes are constantly changing the activation and repression states of geenes in response to current needs and evnironmental conditions: both

Answer 110

major groove

Answer 111

can form heterodimers composed of 2 different members of a family of similarly structured proteins, creating a larger number of functional transcription factors

Answer 112

This provides combinatorial control of gene expression (The use of specific combinations of limited number of regulatory proteins to exert fine control over gene expression)

Answer 113

Genes are still transcribed but the resulting mRNAs are degraded before they can be translated into proteins

Answer 114

base pairing between the antisense oligonucleotide and the target mRNA would prevent recognition by the translation machinery or lead to degradation of the hybrid complex, or both

Answer 115

Careful analysis in the roundworms revealed that protein production was intercepted in the worms after the injection of double stranded RNA when injected with sense or antisense strand alone = normal worms when injected with dsDNA = worms had a twitching phenotype

Answer 116

1. miRNAS are first transcribed as primary miRNA transcripts (pri-mRNAs) with 1 or more sets of internally complementary sequences that can fold to form hairpin-like structures 2. The pri-miRNAs are cleaved by nuclear endonuclease Drosha to produce shortened hairpins (60-70 nucleotides) with a 5' phosphate and a 2-nucleotide 3' overhang - Now known as precursor miRNAs (pre-miRNAs) 3. Pre-miRNAs then bind to export receptor proteins and are transported from the nucleus to the cytoplasm for further processing

Answer 117

siRNA and miRNA

Answer 118

1. In the cytoplasm, pre-miRNAs are cleaved by the Dicer ribonuclease to generate a 20-22 nucleotide ds miRNA. They are then incorporated into a complex called the RNA-induced silencing complex (RISC) which includes the Argonaute (AGO protein) 2. After cleave, the miRNA is unwound and the unneeded passenger strand is discarded 3. The strand complementary to the target is then delivered to a particular mRNA by the AGO protein 4. Once the mRNA has been targeted, the degree of miRNA-mRNA base pairing leads to either Argonaute-mediated degradation (high complementarity) or translational repression (lower complementarity), followed by degradation

Answer 119

cleaved by the Dicer ribonuclease to generate a 20-22 nucleotide ds miRNA

Answer 120

animals = miRNAs are complementary to region in the 3'UTR in the mRNA plants = in the coding region

Answer 121

1. Use a report plasmid to subclone the 3'UTR of the gene of interest downstream of a reporter gene 2. Add the miRNA you want to test 3. Monitor resulting reporter gene expression 4. Loss of expression of your reporter gene = miRNA is binding

Answer 122

1. compete as targets for miRNA binding 2. non-coding RNAs that contain miRNA binding regions - when miRNAs bind to these RNAs instead of their target mRNA, there is a decrease in mRNA repression and increased translation

Module 4 Sections 4-7 Flashcards

Translation Initiation, Elongation, and Termination in Prokaryotes and Eukaryotes, Regulation of Gene Expression, Post-transcriptional Gene Silencing (PTGS) (148 cards)