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BIO 111 > Chapter 13 > Flashcards

Chapter 13 Flashcards

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Biology 101 flashcards
1
Q

gene regulation

A
  • cell can control level of gene expression
  • structural genes are regulated- so proteins produced at certain times and in specific amounts
  • “constitutive” genes are unregulated
  • constant levels of expression
  • “housekeeping genes”
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2
Q

benefits of gene regulation

A
  • conserves energy
  • genes expressed in appropriate cell type and at the correct stage in development
  • results in cell differentiation
  • same genome, different proteomes
  • ex: skeletal muscle cell, neuron and skin cells
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3
Q

Regulation through development

A
  • globin consists of 4 polypeptides
  • composition of hemoglobin protein changes during development
  • fertilization; embryo-> fetus -> adult
  • fetal hemoglobin- higher oxygen affinity
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4
Q

Hoxc8 example

A
  • backbone development
  • nearly identical in several vertebrates
  • but, chicken has 7 vertebrae, mouse has 13
  • why the diversity?
  • transcribed more in mouse
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5
Q

Gene regulation can occur at different points; prokaryotes

A
  1. transcription level regulation
    - common in bacteria
    - controls how much mRNA is made
    - efficient
  2. control rate of translation
  3. regulate at protein or post-translation
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6
Q

gene regulation at different points, eukaryotes

A
  • 4 methods
    1. transcriptional regulation (common)
    2. RNA processing
  • splicing
  • degradation rates
    3. translation
    4. post translation
  • feedback inhibition
  • protein modifications
  • degration rates
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7
Q

transcriptional regulation in bacteria

A
  1. involves regulatory transcription factors
    - bind near promoter, affect trasncription of one or more nearby genes
  2. repressors inhibit transcription
    - negative control
  3. activators increase the rate of transcription
    - positive control
  4. involves small effector molecules
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8
Q

Small effector molecule ; transcriptional regulation in bacteria

A
  • binds to transcription factor-> conformational change
  • no effector-> repressor bound to DNA-> gene off
  • effector-> repressor not bound to DNA-> gene on
  • alters transcription factors ability to bind to DNA
  • 2 domains in transcription factor that respond to small effector molecules
  • site where protein binds to DNA
  • site for small effector molecule binding
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9
Q

Operons

A
  • cluster of genes controlled by one promoter
  • only in prokaryotes
  • genes transcribed together on a single mRNA
  • Polycistronic: different genes ONE mRNA moelcule
  • allows efficient regulation of a group of genes with a common function
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10
Q

what would be the action of a transcription factor that acts an activator?

A

-increase in the number of mRNAs transcribed

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11
Q

lacP

A
  • promoter

- drives expression of multiple genes

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12
Q

lacZ

A

-B-galactosidase: enzyme for catabolizing lactose

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13
Q

lacY

A

lactose permease: enzyme for transporting lactose

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14
Q

lacA

A

galactoside transacetylase- function unknown

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15
Q

near lacP, 2 regulatory sites

A
  1. lacO- operator- provides binding site for repressor protein
  2. CAP site- activator protein binding site
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16
Q

lacl gene

A
  • codes for lac repressor
  • considered a regulatory gene since its sole function is to regulate other genes expression
  • has its own promoter (not part of lac operon)
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17
Q

lac operon: lactose present

A
  • allolactose binds to lac repressor; inactivates repressor

- process called induction and lac operon is inducible

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18
Q

lac operon; lactose absent

A
  • Lac repressor binds to operator site; prevents RNA polymerase from transcribing lacZ, lacY and lacA
  • RNA polymerase can bind but not move forward
19
Q

lac operon; glucose present

A
  • presence of glucose represses the lac operon
  • known as catabolite repression: when the presence of another energy source represses expression of another gene
  • cAMP is a small effector moelcule present ONLY when glucose is absent
  • cAMO binds to an activator protein called catabolite activator protein (CAP)
  • bacteria cannot express lac operon efficiently without CAP
  • high glucose= no cAMP= inactive CAP= no lac transcription
  • hence, no processing of lactose
20
Q

lac operon; glucose low

A
  • cAMP is high
  • cAMP binds/ activates to CAP
  • activated CAP binds to CAP site near lac promoter
  • resulting bend in DNA enhances RNA polymerase binding which increases transcription
21
Q

lac operon; both lactose and glucose high

A
  • lac operon is shut off by low cAMP
  • glucose uptake causes cAMP levels to drop
  • CAP does not activate transcription
  • bacterium uses one sugar at a time, glucose
22
Q

lac operon; lactose is high and glucose is low

A
  • lac operon is turned on
  • allolactose levels rise and prevent lac repressor from binding to operator
  • CAP-cAMP complex is bound to the CAP site
  • bacterium uses lactose
23
Q

transcription regulation in eukaryotes

A
  • follows some of the same principles found in prokaryotes
  • presence of activator and repressor transcription factors (TFs)
  • many TFs regulated by small effector molecules
  • many important differences
  • genes almost always organized individually; no operons!
  • more highly regulated -> increased complexity
24
Q

activators

A

activator proteins stimulate RNA polymerase to initiate transcription

25
Q

repressors

A

repressor proteins inhibit RNA polymerase from initiating transcript

26
Q

modulation (controls gene expression)

A

small effector molecules, protein-protein interactions, and covalent modifications can modulate activators and repressors

27
Q

chromatin (control gene expression)

A

activator proteins promote loosening up of the region in the chromosome where a gene is located, making it easier for RNA polymerase to transcribe the gene

28
Q

DNA methylation (control gene expression)

A

usually inhibits transcription, either by blocking an activator protein or by recruiting proteins that make DNA more compact

29
Q

combinatorial control of gene expression

A

most mechanisms are aimed at controlling the initiation of transcription at the gene promoter

30
Q

3 features in eukaryotic promoters; 1. TATA box

A
  1. TATA box- 25 base pairs upstream from transcriptional start site
31
Q

3 features in eukaryotic promoters; 2. Transcriptional start site

A
  • where transcription begins, with TATA box forms core promoter
  • core promoter alone results in low level basal transcription
32
Q

3 features in eukaryotic promoters; 3. Response elements

A
  • enhancer and silencer transcription factors
  • binding of TFs regulate transcription at the core promoter
  • usually 50-100bps upstream; can be 100,000bps away
33
Q

3 protein complexes needed for transcription

A
  1. RNA polymerase II
  2. general transcription factors
    - GTFs + RNA Pol II come together at core promoter before transcription initiation
    - pre initiation complex- assembled GTFs and RNA Pol II at the TATA box; form basal transcription apparatus
  3. mediator- composed of several proteins
    - partially wraps around GTFs and RNA Pol II
    - mediates interactions with activators or repressors
    - controls rate at which RNA Pol II can begin transcription
34
Q

response elements control of transcription

A
  • activators bind to enhancer sequences
  • repressors bind to silencer sequences
  • regulate rate of transcription of a nearby gene
  • most TFs do not bind directly to RNA Pol II
35
Q

3 ways to control RNA polymerase II

A
  1. By promoting the assembly of the pre initiation complex
    - results in a basal rate of transcription
  2. control rate of RNA Pol II transcription via mediator
    - activators “turn-on” mediator-> increased transcription
    - repressors “turn-off” mediator -> decreased transcription
  3. recruit proteins that influence DNA packaging
    - DNA is NOT naked
    - proteins bind and compact DNA into chromatin
    - packaging affects gene expression
    - whether RNA Pol can “get” to a gene
    - heterochromatin vs. euchromatin
36
Q

unpacking DNA

A
  • some activators “unwind” DNA near a gene
  • recruit proteins to loosen DNA compaction
  • histone acteyltransferase (HAT) attaches acetyl groups to histone proteins so they don’t bind DNA as tightly
37
Q

DNA methylation- turning genes off

A
  • DNA methylase attaches methyl groups to DNA
  • usually inhibits transcription
  • common in some eukaryotes but not all
  • generally occurs at “CpG islands”
  • region of high C and G phosphodiester bonds
  • near promoters in vertebrates and plants
  • methylated CpG islands are correlated with repressed genes
38
Q

Methylation inhibits transcription in 2 ways

A
  1. methylation of CpG islands prevents activator binding

2. converts chromatin fro open to closed

39
Q

regulation of RNA processing and translation in eukaryotes

A
  • unlike bacteria, gene expression commonly regulated by RNA processing
  • added benefits include
  • produce more than one mRNA transcript from a single gene (gene encodes 2 or more polypeptides)
  • more complex proteome can be made
  • faster regulation achieved by controlling steps after mRNA transcript made
  • alternative splicing
40
Q

alternative splicing of pre-mRNAs

A
  • causes mRNAs to contain different patterns of exons
  • alternative proteins generally have similar functions
  • allows same gene to make different proteins
  • at different stages of development
  • in different cells types
  • in response to a change in the environmental conditions
41
Q

splicing across evolutionary history

A

frequency of alternative splicing increases with increasing biological complexity

42
Q

translational regulation- miRNAs

A
  • microRNAs (miRNAs)- AKA RNA interference (RNAi)
  • small RNA molecules that silence translation of mRNAs
  • degrade mRNA or block translation
  • common in animals and plants
43
Q

translational regulation: iron binding example

A
  • iron= cofactor for many enzymes
  • but toxic at high levels
  • mammalian cells make protein ferritin
  • forms a hollow, spherical complex to store excess iron
  • translation of the mRNA that codes for ferritin is controlled by an RNA-binding protein known as the iron regulatory protein (IRP)
44
Q

different levels of iron

A
  • when iron levels in the cytosol are low, ferritin is not needed
  • IRP binds to a response element within the ferritin mRNA
  • inhibits translation
  • when iron is abundant, iron binds to IRP and prevents it from blocking translation
  • ferritin mRNA is translated to make more ferritin protein
  • faster than transcriptional regulation, which requires activation, transcription, and translation of ferritin gene

BIO 111 (17 decks)

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