Molecular Genetics: Gene Expression

Question 1

gene expression

Answer 1

when DNA information is converted into functional molecules

Question 2

constitutive expression

Answer 2

always expressed

Question 3

regulated expression

Answer 3

expressed sometimes or in some cells

Question 4

regulation can occur at which levels

Answer 4

transcriptional, translational, post-translational

Question 5

which level of regulation has the most immediate effect

Answer 5

post-translational, but energy costly

Question 6

which level of regulation is the most energy efficient

Answer 6

transcriptional, but slow effect

Question 7

transcriptional regulation

Answer 7

regulatory proteins bind to DNA and inhibit or trigger transcription

Question 8

translational regulation

Answer 8

change in mRNA stability or change in translation speed

Question 9

post-translational regulation

Answer 9

chemical modifications of protein

Question 10

negative control

Answer 10

genes turned off by a repressor protein bound to the operator sequence (i.e. lac operon)

Question 11

operon

Answer 11

set of co-regulated genes which share promoter and regulatory sequence and are co-transcribed onto single mRNA strand

Question 12

how does glucose regulate the lac operon

Answer 12

inducer exclusion via allosteric regulation of the permease transport proteins

Question 13

inducer

Answer 13

triggers gene expression (i.e. lactose in lac operon)

Question 14

inducible negative regulation

Answer 14

lac operon - repressor blocks gene expression, inducer inhibits functioning of the repressor

Question 15

repressible negative regulation

Answer 15

trp operon - trp (inducer) binds to repressor to allow the repressor to bind to the operator and block gene expression

Question 16

positive control

Answer 16

gene expression turned on by activator protein binding to an initiator sequence (araoperon)

Question 17

how is the ara operon positvely regulated

Answer 17

when arabinose is present binding of araC protein to initiator allows for transcription of araBAD

Question 18

how is the ara operon negatively regulated

Answer 18

when arabinose is absent araC protein is in different conformation that binds to ara operon initiator and araC operator to block transcription of both

Question 19

global gene regulation

Answer 19

coordinating expression of large sets of genes

Question 20

examples of global gene regulation in prokaryotes

Answer 20

operons, sigmas, regulons

Question 21

sigmas

Answer 21

different sigmas activated in reponse to envrionment - binds to different promoters to activate different groups of genes

Question 22

regulons

Answer 22

sets of genes or operons that have separate promoters but are controlled by the same regulatory protein that bind to the same but separate regulatory sequences

Question 23

SOS response under negative control

Answer 23

repressor lexA bound to the operators; in response to DNA damage the protein recA induces lexA to allow transcription of repair genes

Question 24

two groupings of gene regulation in eukaryoets

Answer 24

regulation in the nucleus

regulation in the cytoplasm

Question 25

methods for regulation in the nucleus of eukaryotes

Answer 25

transcriptional control, chromatin remodeling, RNA processing

Question 26

methods for regulation in the cytoplasm of eukaryotes

Answer 26

mRNA stability, translational control, post-translational modifications

Question 27

nucleosomes

Answer 27

"beads" of DNA wrapped around histones link by "string" of 80bp DNA linker

Question 28

core histones

Answer 28

2 H2A-H2B dimers and H3-H4 tetramer

Question 29

H1

Answer 29

linker histone that seals DNA to the core histones

Question 30

chromatin condensing

Answer 30

nucleosomes interact to form a 30nm fiber - loops around protein scaffold - condenses even further to form chromosomes during mitosis

Question 31

DNA methylation

Answer 31

DNA methyltransferase (DMT) adds methyl groups to DNA

Question 32

increased DNA methylation resuls in

Answer 32

condensed chromatin - reduced gene epression

Question 33

histone code hypothesis

Answer 33

gene expression is in part regulated by combination of chemical modification on histones

Question 34

histone-acetyl transferases (HATs)

Answer 34

add negatively charged acetyl groups to lysines in histone proteins

Question 35

how do HATs effect chromatin

Answer 35

acetyl groups weaken interaction between histone and DNA - chromatin decondensing

Question 36

chromatin remodeling complexes

Answer 36

use ATP to slide nucleosome along DNA or eject histones from chromatin to open up DNA for transcription

Question 37

transcription activators

Answer 37

bind to enhancers to recruit chromatin remodeling complexes to the correct place for transcription initiation

Question 38

epigenetic inheritence

Answer 38

patterns of inheritence that do not relate to the primary sequence of DNA

Question 39

maternal effects

Answer 39

mother's environment can cause changes to chromatin in offspring during development that have lasting effects on offspring's gene expression

Question 40

enhancers

Answer 40

regulatory sequence that activates transcription when bound by an activator

Question 41

silencers

Answer 41

regulatory sequence that inhibits transcription when bound by a repressor

Question 42

whats special about silencers and enhancers

Answer 42

unique to eukaryotes, can be far away from gene its regulating, can work if flipped backwards

Question 43

promoter-proximal elements

Answer 43

regulatory sequences that bind transcription factors and are located close to the promoter

Question 44

in eukaryotes co-regulated genes can share

Answer 44

enhancer, silencer, promoter-proximal element

Question 45

mediator

Answer 45

binds to basal and regulatory transcription factors

Question 46

splice variants

Answer 46

alternatively spliced primary transcripts

Question 47

isoforms

Answer 47

different proteins dependent on splice variants

Question 48

splicing factors

Answer 48

proteins that bind to RNA and can activate or repress splicing at specific sites

Question 49

mRNA stability

Answer 49

how long a mRNA stays intact - degradation occurs with removal of the tail or cap

Question 50

what maintains mRNA stability

Answer 50

regulatory proteins that can bind to mRNA

Question 51

RNA interference pathway

Answer 51

microRNAs or small interfering RNAs that bind to mRNA to target it for destruction or inhibits translation

Question 52

dicer

Answer 52

enzyme that cuts precursor miRNA or siRNA

Question 53

how do miRNAs and siRNAs interect with mRNA

Answer 53

guide strand binds to Argonaute protein which binds to target mRNA

Question 54

RISC

Answer 54

RNA induced silencing complex (mi/siRNA and Argonaute and other proteins)

Question 55

source of siRNA

Answer 55

endogenous (experimental) or exogenous (viral) double-stranded RNA

Question 56

specificity of siRNA

Answer 56

targets 1 RNA and binds specifically to target

Question 57

result of siRNA

Answer 57

mRNA degradation

Question 58

source of miRNA

Answer 58

small double stranded RNAs in the nucleus

Question 59

specificity of miRNA

Answer 59

targets multiple RNAs and has less specific binding

Question 60

result of miRNA

Answer 60

mRNA degradation or translation inhibition

Question 61

why is the RNAi pathway useful in biotech?

Answer 61

knock out mutants can be made without completely altering a gene

Question 62

what levels of gene regulation do eukaryotes have that prokaryotes don't have

Answer 62

chromatin remodeling, RNA processing, mRNA stability

Question 63

what happens when RISC-miRNA binds to 3' UTR

Answer 63

translation initiation blocked because formation of translation initiation factor complex is prevented

Question 64

what happens when RISC-miRNA binds to a different region of the mRNA

Answer 64

translation elongation is blocked

Question 65

methods of cell-wide reduction of translation

Answer 65

phosophorylation or ribosomes or EIFs (in translation initiation factor complex)

Question 66

ubiquitin-mediated proteolysis

Answer 66

proteins tagged with ubiquitin by ubiquitin ligases are recognized by the proteosome for destruction