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Spring 2025 > Cell Molecular Exam 2 > Flashcards

Cell Molecular Exam 2 Flashcards

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1
Q

What is the primary means of regulating gene expression?

A

Transcription

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2
Q

How do promoters regulate transcription?

A

Promoters are DNA sequences

Initiate transcription by providing a binding site for RNA polymerase.

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3
Q

How do promoter-proximal elements regulate transcription?

A

Promoter-proximal elements are DNA sequences

Located close to the promoter that enhances transcription efficiency.

Bind to activator or repressor transcription factor.

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4
Q

How do enhancers regulate transcription?

A

Enhancers are DNA

That can increase transcription levels from a distance by interacting with transcription factors.

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5
Q

How do transcription activators regulate transcription?

A

Transcription activators are proteins

That bind to specific DNA sequences to promote the recruitment of RNA polymerase.

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6
Q

How do transcription repressors regulate transcription?

A

Transcription repressors are proteins

That bind to DNA and inhibit transcription by blocking RNA polymerase access.

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7
Q

What are the 3 eukaryotic nuclear RNA polymerases?

A

RNA polymerase I synthesizes rRNA, RNA polymerase II synthesizes mRNA, and RNA polymerase III synthesizes tRNA.

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8
Q

Compare and contrast TATA box and CpG island promoters.

A

TATA box - high levels of transcription, activated by TATA box binding protein, works as an on-off switch.

CpG island - alternating C and G, always being transcribed, higher or lower based on methylation.

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9
Q

How do negative elongation factors NELF and DSIF regulate RNA polymerase II?

A

NELF and DSIF pause RNA polymerase II during transcription elongation, allowing for additional regulatory mechanisms.

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10
Q

Describe the structure and function of C2H2 zinc finger.

A

C2H2 zinc fingers are protein domains that bind to DNA and play a role in transcription regulation.

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11
Q

Describe the structure and function of leucine zipper.

A

Leucine zippers are protein motifs that facilitate dimerization and DNA binding in transcription factors.

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12
Q

Describe the structure and function of bHLH.

A

bHLH (basic Helix-Loop-Helix) domains are involved in DNA binding and dimerization for transcription regulation.

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13
Q

How do histone acetylases affect transcription?

A

Histone acetylases add acetyl groups to histones, leading to a more open chromatin structure and increased transcription.

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14
Q

How do histone deacetylases affect transcription?

A

Histone deacetylases remove acetyl groups from histones, resulting in a closed chromatin structure and decreased transcription.

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15
Q

What is the role of the Mediator complex?

A

The Mediator complex acts as a bridge between transcription factors and RNA polymerase II to facilitate transcription initiation.

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16
Q

How do nuclear receptors activate transcription in response to extracellular signals?

A

Nuclear receptors are activated in the cytoplasm, and then move to the nucleus and start transcription.

Nuclear receptors bind to ligands and undergo conformational changes that allow them to interact with DNA and activate transcription.

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17
Q

What are the roles of the Polycomb and Trithorax complexes?

A

Polycomb - maintains repressed expression.
Trithorax - inhibits polycomb, demethylated.
Early embryonic development. specifically involved in the development of the anterior and posterior end, through epigenetic expression.

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18
Q

What takes place during mRNA capping?

A

Happens first, involves the addition of a 7-methylguanylate cap to the 5’ end of mRNA, occurring co-transcriptionally.

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19
Q

What takes place during mRNA splicing?

A

Splicing removes introns from pre-mRNA and joins exons together, occurring in the nucleus.

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20
Q

What takes place during cleavage/polyadenylation?

A

Cleavage/polyadenylation adds a poly(A) tail to the 3’ end of mRNA, enhancing stability and export.

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21
Q

What is the structure and function of the RNA polymerase II CTD?

A

The CTD is a repetitive domain on RNA polymerase II that coordinates mRNA processing events during transcription.

One end of protein forms long end of tail, interictally ordered domain, 7 amino acids repeated 53 times, controls RNA processing, partly responsible for transcription rate.

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22
Q

What sequence is found at the 5’ splice site?

A

The 5’ splice site typically contains a GU sequence, recognized by the spliceosome.

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23
Q

What sequence is found at the 3’ splice site?

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A

The 3’ splice site typically contains an AG sequence, recognized by the spliceosome.

24
Q

What is the branchpoint sequence?

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A

The branchpoint sequence is an A residue that plays a crucial role in the splicing reaction.

has A nucleotide

25
What is the poly(A) site sequence?
The poly(A) site is recognized by the cleavage and polyadenylation machinery, typically containing a AAUAAA sequence. 3' end of the pre-mRNA
26
How do alternative splicing and alternative polyadenylation allow expression of different mRNAs from the same gene?
Alternative splicing can produce different mRNA isoforms by including or excluding exons, while alternative polyadenylation can generate mRNAs with different 3' ends. Two possible poly a site resulting in different transcription sites r
27
What is the role of SR proteins in regulating alternative splicing?
SR proteins promote splicing by binding to exonic splicing enhancers and facilitating the assembly of the spliceosome. Protein, splicing protein (serine and argine rich proteins)
28
What are exonic splicing enhancers (ESEs)?
ESEs are sequences within exons that enhance the recognition of splice sites and promote splicing. Sequence, bound by SR proteins, then recruits the spliceosome to increase splicing at the site.
29
What is the function of the exosome?
The exosome is a multi-protein complex that degrades RNA molecules in the cytoplasm.
30
How can an error in splicing lead to disease?
It can bypass the quality control and get exported, HIV is an example. Another example is cancer, where splicing is mutated so splicing still happens but changes the sites.
31
How does the cell control export of an mRNA to the cytoplasm?
The cell uses nuclear transport receptors to recognize and transport processed mRNA from the nucleus to the cytoplasm.
32
What are the 3 pathways of mRNA degradation in the cytoplasm?
The three pathways are: Decapping - (dependent) shortens the tail, decapping, exonuclease polyatail gradually gets removed, then RNA is degraded Deadenylation - Independent mRNA, decapping bypassing poly-A tail. Endonucleolytic cleavage - cut in the middle of RNA, exonuclease degrades in both directions.
33
Compare and contrast miRNAs and siRNAs.
miRNAs are typically involved in regulating gene expression by binding to target mRNAs. Inhibit translation, seed sequence matches but rest doesn’t siRNAs are often derived from long double-stranded RNA and mediate RNA interference. Degrade, perfectly complementarily Both involved in gene expression.
34
What is nonsense-mediated decay?
Nonsense-mediated decay is a surveillance mechanism that degrades mRNAs containing premature stop codons. (nonsense mutation causes stop codon) RNA gets degraded before it creates a protein, scanning to reach a stop codon.
35
Give an example of mRNA localization to specific areas of the cell.
mRNAs can be localized to dendrites in neurons to ensure localized protein synthesis. goes to one end of the cell to allow for cleavege to occur that results in different mother daughter DNA for futrue generations.
36
How is rRNA transcribed and processed?
rRNA is transcribed by RNA polymerase I and processed in the nucleolus, involving cleavage and modification.
37
What modifications are made to rRNA?
Base modifications to yield mature 28S, 18S, and 5.8S rRNAs that associate with ribosomal proteins
38
What is the role of snoRNPs?
snoRNPs are small nucleolar ribonucleoproteins that guide the chemical modifications of rRNA.
39
How are tRNAs transcribed and processed?
tRNAs are transcribed by RNA polymerase III and undergo processing that includes 5' capping, splicing, and 3' addition of the CCA sequence. Pre-tRNAs synthesized by RNA polymerase III and processed in the nucleoplasm.
40
What is a nuclear body?
Not membrane-bound organelles, but locations where specific things occur. Nucelous Cajal bodies - storage and making splicesome protein Ppeckle - splicing stored Histone locus body - histone transcription and processing Paras pekle
41
What chemical properties of phospholipids cause them to form lipid bilayers?
Phospholipids have hydrophilic heads and hydrophobic tails, leading to the formation of bilayers in aqueous environments.
42
What are the 3 primary lipid components of biomembranes?
Phospholipids, Sphingolipids, and Cholesterol
43
What is the fluid mosaic model of biomembrane structure?
The fluid mosaic model describes the cell membrane as a dynamic structure with various proteins floating in or on the fluid lipid bilayer.
44
How are the two leaflets of the cell membrane identified?
By their distinct lipid compositions and the orientation of membrane proteins.
45
How does phosphoglyceride content affect membrane properties?
Higher phosphoglyceride content generally increases membrane fluidity. Thinner membrane.
46
How does sphingomyelin content affect membrane properties?
Sphingomyelin content can increase membrane thickness and stability. Thicker membrane.
47
How does cholesterol content affect membrane properties?
It can increase the range of the melting temperature. Cholesterol maintains membrane fluidity by preventing fatty acid chains from packing too closely.
48
How does fatty acid chain length affect membrane properties?
Longer fatty acid chains can increase membrane thickness and decrease fluidity. More rigid the chain will be.
49
How does fatty acid saturation affect membrane properties?
Saturated fatty acids tend to make membranes less fluid compared to unsaturated fatty acids. More rigid the chain will be.
50
How does polar head group size affect membrane properties?
Larger polar head groups can increase membrane curvature and affect bilayer stability.
51
What are lipid rafts?
Lipid rafts are in the cell membrane, are a mix of lipids and proteins that move as a unit.
52
What 3 kinds of proteins are associated with cell membranes?
Integral proteins span the membrane. Peripheral proteins are attached to the surface. Lipid-anchored proteins are covalently linked to lipids.
53
How are phospholipids transferred from one leaflet to the other?
Phospholipids are transferred by flippases, which do it, they are synthesised in one leaflet. Leaflets are asymmetrical. The flipase intentionally does this.
54
What is the rate-limiting enzyme in the cholesterol biosynthesis pathway?
HMG-CoA reductase is the rate-limiting enzyme in cholesterol biosynthesis.
55
What is the function of FABPs?
Move fatty acids across the cell. Fatty acid-binding proteins (FABPs) transport fatty acids within cells and play roles in lipid metabolism.
56
What do each of the polymerases make?
Pol 1 - rRNA Pol 2 - pre-mRNA, snRNA, miRNA Pol 3 - tRNA

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