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Genetics EXAM 3 > Chapter 11 - Eukaryote Gene Expression Control > Flashcards

Chapter 11 - Eukaryote Gene Expression Control Flashcards

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1
Q

Key to Eukaryotic Complexity

A

The complexity of eukaryotes is due to fine-tuned regulation of gene expression, not more genes.

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2
Q

Coding DNA vs. Regulatory DNA

A

Only about 2% of the human genome codes for RNA or protein; the remaining ~25% contains cis-acting elements that regulate gene expression.

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3
Q

Housekeeping Genes

A

Housekeeping genes are constitutively expressed (always on) because they are essential for basic cellular functions, such as energy metabolism and protein synthesis.

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4
Q

Tissue-Specific Genes

A

Some genes are expressed only in specific cell types or under certain conditions (e.g., hemoglobin in red blood cells, myoglobin in muscle cells).

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5
Q

Levels of Gene Expression Regulation

A

Gene expression can be regulated at the level of transcription, RNA processing, translation, and post-translational modifications.

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6
Q

Trans-acting Factors

A

Trans-acting factors are proteins (often transcription factors) that regulate gene expression by interacting with cis-acting elements.

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7
Q

Cis-acting Elements

A

Cis-acting elements are DNA sequences (promoters, enhancers, silencers) that control gene expression at specific locations.

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8
Q

Regulation at Transcription Level

A

Most eukaryotic gene expression regulation occurs at the transcription level, through interactions between trans-acting factors and cis-acting elements.

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9
Q

Gene Expression Layers

A

Gene expression is regulated at multiple levels: DNA level, transcription, RNA processing, translation, post-translational modifications, and protein stability.

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10
Q

Gene/DNA Level Regulation

A

Promoters, enhancers, silencers, and insulators control transcription initiation and gene expression.

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11
Q

Transcription Regulation

A

Transcription factors and co-activators bind to cis-acting elements in DNA. Epigenetic modifications (like DNA methylation) and chromatin remodeling affect transcription.

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12
Q

RNA Processing & Stability

A

Includes splicing, 5’ capping, polyadenylation, and RNA export. RNA stability (mRNA half-life) controls how long RNA is available for translation.

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13
Q

Translational Regulation

A

Translation initiation and speed of translation regulate protein production. Regulatory elements (like UTRs) can influence translation efficiency.

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14
Q

Protein Activation

A

Post-translational modifications (e.g., phosphorylation, acetylation) activate/inactivate proteins. Subcellular location of proteins regulates their function.

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15
Q

Protein Stability

A

Protein half-life varies—some proteins are very stable, while others are rapidly degraded.

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16
Q

Function of RNAs

A

mRNA serves as a template for translation. Non-coding RNAs (miRNA, siRNA) regulate gene expression at transcriptional/post-transcriptional levels.

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17
Q

Types of RNA Polymerase

A

-RNA Pol I: Transcribes rRNA genes.
- RNA Pol II: Transcribes mRNA (protein-coding genes).
- RNA Pol III: Transcribes tRNA genes.

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18
Q

Cis-acting Elements

A
  • Promoters: Directly involved in transcription initiation.
  • Enhancers: Increase transcription from a distance.
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19
Q

Core Promoter

A

-Contains TATA box, CAAT box, and CpG islands.
- Basal transcription factors bind to this region to recruit RNA Pol II.

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20
Q

TATA Box

A
  • A conserved sequence (TATAAT) found around -30 from the transcription start site. Important for RNA Pol II binding.
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21
Q

CAAT Box

A
  • A conserved sequence often found upstream of the TATA box that is involved in transcription regulation.
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22
Q

CpG Islands

A

-Regions rich in CG dinucleotides, often located near promoters and involved in gene regulation.

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23
Q

Basal Transcription Factors

A
  • TBP binds to TATA box.
  • TAFs bind to TBP and recruit RNA Pol II. This forms the pre-initiation complex.
  • Allows for low basal transcription.
  • proteins that are essential for gene transcription to occur
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24
Q

Enhancers

A
  • DNA sequences that regulate gene expression by binding transcription factors (TFs).
  • Act as either activators or repressors.
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25
Q

Core Promoter vs Enhancers

A
  • Core promoter: Same for all genes of a given RNA polymerase type, includes basal transcription factors (basal machinery).
  • Enhancers are gene-specific and have unique TF binding sites
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26
Q

Location of Enhancers

A
  • Enhancers can be upstream, downstream, or within introns of the gene they regulate.
  • They can act over kilobases (kb) away from the promoter.
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27
Q

Multiple Promoters

A
  • One enhancer can regulate multiple promoters/genes unless insulators prevent interaction.
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28
Q

Function of TFs in Enhancers

A
  • Activators: Bind to enhancers to enhance transcription.
  • Repressors: Bind to enhancers to decrease transcription.
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29
Q

Transcriptional Activators

A
  • Bind to specific DNA sequences (motifs) in enhancers.
  • Often referred to as consensus sequences or binding sites.
30
Q

Role of Activators

A
  • Increase transcription by promoting the assembly of the transcription machinery.
  • Recruit mediators and co-activators.
31
Q

Mediators and Co-activators

A
  • Mediators bridge TFs and basal transcription machinery (RNA polymerase II).
  • Co-activators help bring enhancers and promoters together.
32
Q

DNA Bending by Co-activators

A
  • Most co-activators bend the DNA to facilitate the interaction between enhancers and promoters.
33
Q

Chromatin Remodeling by Co-activators

A
  • Some co-activators perform histone modification (usually histone acetylation through HATs).
  • Nucleosome shuffling exposes the promoter.
34
Q

Transcriptional Repressors

A
  • Bind to specific sites within enhancers.
  • Inhibit gene expression by preventing the recruitment of transcription machinery.
35
Q

Co-repressors

A
  • Recruited by repressors.
  • Block transcription in two ways:
    1) Disrupt basal machinery.
    2) Remodel chromatin (via HDACs).
36
Q

Chromatin Remodeling by Co-repressors

A
  • Histone deacetylases (HDACs) remove acetyl groups from histones, making the chromatin more tightly packed, thus reducing transcription.
37
Q

Indirect Repression Mechanisms

A
  • Competition with activators: Repressors compete with activators for binding sites.
  • Direct binding to activators: Repressors block activators.
38
Q

Dual Role of Transcription Factors

A

Some transcription factors can act as both activators and repressors, depending on the context (such as the presence of co-factors).

39
Q

Sequence Motifs

A
  • Proteins bind to DNA at specific “motifs”
    Not an exact sequence, but a series of “preferences”
    Some bp positions are strict, others are flexible
    You will often hear “consensus sequence,” this is a BAD concept
40
Q

Nuclear Receptors

A
  • Hydrophobic hormones (e.g., steroid hormones, thyroid hormones, vitamin D) bind to nuclear receptors inside the cell.
41
Q

Hormone Binding

A
  • Hormones bind to nuclear receptors, causing a conformational change that activates the receptor.
42
Q

Dimers

A
  • Upon hormone binding, nuclear receptors often form dimers (homo- or hetero-dimers).
43
Q

Response Elements

A
  • Dimers bind directly to specific DNA motifs called response elements, typically in the promoter/enhancer regions of target genes.
44
Q

Activators vs. Repressors

A
  • Nuclear receptors can act as activators or repressors based on the proteins they recruit.
  • Activators enhance transcription, while repressors block it.
45
Q

Insulators

A
  • DNA sequences that block enhancer-promoter interactions.
  • Organize DNA into loops.
46
Q

Insulator Sequence Example

A
  • CCGCGNGGNGGCAG is the binding site for CTCF (CCCTC-binding factor).
47
Q

Function of Insulators

A
  • Form boundaries for an enhancer’s effects.
  • Prevent spreading of heterochromatin into active gene regions.
48
Q

DNA Loops

A
  • An enhancer and promoter must be in the same loop to interact.
  • Loops are the units of transcriptional regulation by enhancers.
49
Q

CTCF Binding and Loop Formation

A
  • CTCF binds to insulator sequence and forms a loop by interacting with other distant CTCF proteins.
  • This looping regulates enhancer-promoter interactions
50
Q

Noncoding RNAs (ncRNAs)

A
  • RNAs that do not code for proteins.
  • Regulate gene expression and other cellular functions.
  • Majority of RNA in a cell is ncRNA.
51
Q

Long Noncoding RNAs (lncRNAs)

A
  • > 200bp in length.
  • Involved in gene regulation, many with unknown functions.
  • Example: Xist (X-inactivation, Barr body formation).
52
Q

Short Noncoding RNAs (<200bp)

A
  • miRNAs: Regulate gene expression via RNA interference (RNAi).
  • siRNAs: Similar to miRNAs, also involved in RNAi.
  • piRNAs: Silence transposable elements in germline cells.
53
Q

Other Short ncRNAs

A
  • snoRNAs: Involved in rRNA maturation and ribosome assembly.
  • snRNAs: Involved in mRNA splicing.
  • tRFs: Derived from tRNAs, function still under investigation.
54
Q

RNA Interference (RNAi)

A
  • miRNAs and siRNAs induce gene silencing through degradation or translation inhibition of target mRNAs.
55
Q

RNA Interference (RNAi)

A
  • A process of gene silencing through inhibition of translation or mRNA degradation.
  • Involves miRNAs and siRNAs.
  • A major mechanism of post-transcriptional regulation.
56
Q

miRNAs

A
  • Derived from long primary RNA (pri-miRNA), processed into shorter hairpin structures (pre-miRNA).
  • Play a role in regulating gene expression.
57
Q

siRNAs

A
  • Produced from double-stranded RNA (e.g., viral RNA), acting similarly to miRNAs.
  • Involved in gene silencing through RNA degradation or translation inhibition.
58
Q

Target Mechanism

A
  • miRNAs/siRNAs bind to complementary 7-bp sequences in the 3’-UTR of target mRNAs.
  • Perfect match → destruction of mRNA, mismatch → translation attenuation.
59
Q

RISC Complex

A

a multiprotein complex that regulates gene expression by silencing RNA

60
Q

miRNA Processing

A
  1. Pri-miRNA: Long primary transcript.
  2. Pre-miRNA: Short hairpin structure.
  3. RISC Complex Loading: One or both strands of pre-miRNA are incorporated into RISC.
61
Q

miRNA Targeting in Humans

A
  • Over 1600 miRNA genes in humans.
  • miRNAs can target hundreds of genes.
  • ~60% of protein-coding genes targeted by at least one miRNA.
62
Q

Post-Translational Modifications (PTMs)

A
  • Modifications made to proteins after translation to regulate function, stability, and interactions.
  • Common in eukaryotes, rare in prokaryotes.
63
Q

Proteolysis (Cleavage)

A
  • N-terminal Methionine Removal: Over 60% of proteins lose the first amino acid (methionine).
  • Some proteins are polyproteins that get cleaved into smaller proteins.
64
Q

Zymogens

A
  • Inactive enzymes that require cleavage to become active.
  • Examples: digestive enzymes, lysosomal enzymes.
65
Q

Phosphorylation

A
  • Addition of phosphate group to serine, threonine, or tyrosine.
  • Regulates protein activity (on/off switch).
  • Kinase adds phosphate, phosphatase removes it.
66
Q

Glycosylation

A
  • Addition of sugar groups (carbohydrates) to proteins.
  • Affects protein folding, stability, and signaling.
67
Q

Ubiquitination

A
  • Addition of ubiquitin to proteins, signaling their degradation.
  • Targets proteins for degradation via the proteasome.
67
Q

Lipidation

A
  • Addition of lipid groups (e.g., fatty acids) to proteins.
  • Mediates membrane anchoring and signal transduction.
68
Q

Polypeptide becomes

A

Protein, once it has been folded into its shape

69
Q

Kinase

A

an enzyme that adds phosphates

70
Q

Phosphates

A

act as an on and off for proteins

Genetics EXAM 3 (4 decks)

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