eukaryotic transcription 2

What is the main role of transcription factors (TFs)?

They decide whether transcription happens, which genes are expressed, and when (e.g. in response to signals) 🎛️.

Why are transcription factors hard to study experimentally?

They are low-abundance proteins present in very small amounts 🧪.

What determines a transcription factor’s function?

Its amino acid sequence and 3D structure 🧠.

How can transcription factors be identified using bioinformatics?

By finding conserved DNA sequences near genes that suggest TF binding sites 💻.

How can we use mutations to analysis and help identify transcription factors?

By mutating promoter or USE sequences and observing changes in transcription 🔧.

How were transcription factors classically isolated?

Using DNA affinity chromatography to purify proteins that bind specific DNA sequences 🧲.

What classic experiment identified Sp1?

Tjian (1986) used GC-box DNA to isolate Sp1 from HeLa cells 🧬.

What does it mean that transcription factors are modular proteins?

They have separate DNA-binding and regulatory domains that work independently 🧩.

Why does DNA binding alone not activate transcription?

Because activation requires a separate activation domain to interact with transcription machinery ⚠️.

What are the three major types of DNA-binding domains in transcription factors?

Zinc fingers ✋,

helix–turn–helix 🌀,

and basic (positively charged) domains ➕.

What is a zinc finger DNA-binding domain?

A ~23 amino acid loop stabilised by Zn²⁺ that uses an α-helix to bind DNA, usually in the major groove 🧷.

Does zinc bind DNA directly in zinc finger proteins?

No — Zn²⁺ stabilises protein folding, not DNA binding ❌.

Which transcription factor is a classic zinc finger protein?

Sp1 🧬.

What is a helix–turn–helix (HTH) DNA-binding domain?

Two α-helices where one “recognition helix” binds the major groove of DNA 🔍.

How do HelixTturnHelix proteins bind DNA?

As dimers, with recognition helices spaced one DNA turn apart 🔗.

What are homeodomains?

A type of HTH domain (~60 aa, 3 α-helices) important for developmental gene regulation 🧠.

What is a basic DNA-binding domain?

A positively charged domain in the TF that cannot bind DNA alone and must dimerise ➕.

What are the two main types of basic DNA-binding domains?

Leucine zipper 🤐 and helix–loop–helix 🔁.

Which transcription factor is an example of a basic zipper protein?

C/EBP 🧬.

How are ligand-dependent transcription factors regulated?

They are inactive without ligand and become active after ligand binding 🎯.

Where are steroid hormone receptors located before activation?

In the cytoplasm or nucleus, but inactive 🚫.

What structural feature do steroid hormone receptors contain?

Cys₂–Cys₂ zinc fingers ✋.

What happens when a ligand binds a steroid hormone receptor?

Conformational change 🔄, dimerisation 🤝, nuclear localisation 🚪, DNA binding.

Give examples of ligand-dependent transcription factors.

VDR, GR, ER, AR 🧪.

What is an activation domain?

A region of a TF that stimulates transcription but does not bind DNA ⚡.

Do activation domains have a fixed 3D structure?

No — they are flexible and defined by amino acid composition 🧠.

What are the three common types of activation domains?

Acidic ⚡, glutamine-rich 🧬, and proline-rich 🧱.

How do activation domains stimulate transcription?

By interacting directly with the PIC or recruiting co-activators 🤝.

Which PIC components can activation domains interact with?

TBP and TAFs 🧩.

What are co-activators?

Proteins that do not bind DNA but link TFs to transcription machinery and modify chromatin 🔗.

Why is chromatin structure important for transcription?

Tightly packed chromatin blocks access to DNA and represses transcription 🧶.

How do histone acetyltransferases (HATs) activate transcription?

They acetylate lysines, reduce histone positive charge, and loosen chromatin 🔓.

Why does histone acetylation loosen chromatin?

It weakens histone–DNA interactions by neutralising charge ⚖️.

What is p300/CBP?

A major co-activator with HistonAcetylTransferase activity recruited by steroid hormone receptors 🏗.

Which histones are acetylated by p300/CBP?

H3, H4, H2A, and H2B 🧬.

What is an inhibitory (repressor) domain?

A TF domain that reduces or shuts down transcription 🚫.

List three mechanisms of transcriptional repression.

Blocking activator binding ✋, blocking the PIC 🧱, or recruiting co-repressors 🧲.

What do histone deacetylases (HDACs) do?

Remove acetyl groups, tighten chromatin, and repress transcription 🔒.

What is SMRT?

A co-repressor that works with HDAC1/2 to repress transcription 🧩.

How does SMRT repress transcription?

It recruits HDACs and stabilises interactions that block transcription ❌.

Why is tamoxifen clinically important?

It is an oestrogen receptor antagonist used in breast cancer treatment 💊.

How does tamoxifen inhibit transcription?

It forces ER into a conformation that recruits co-repressors instead of co-activators 🚫.

Why can tamoxifen resistance occur in some cancers?

Some cancers recruit co-activators even when tamoxifen is present ⚠️.

What is the key takeaway about transcription factor regulation?

Transcription depends on TF structure, chromatin state, and co-activator or co-repressor recruitment 🧠.