How can methylation of mammalian promoter CpG islands repress transcription?

It can recruit methyl-CpG-binding repressors and chromatin-modifying proteins, often reducing promoter accessibility and transcription. The effect depends on genomic and cellular context.

Which common bacterial ribosome-binding element helps position the start codon?

The Shine–Dalgarno sequence, often represented by the AGGAGG consensus, pairs with the 3′ end of 16S rRNA. Not all bacterial mRNAs use this element.

Which complex uses miRNA or siRNA guides to silence target mRNAs?

RISC, the RNA-induced silencing complex, contains an Argonaute protein that binds the guide. Silencing can involve RNA cleavage, decay or translational repression; not every Argonaute has slicing activity.

Why do ddNTPs terminate DNA synthesis in Sanger sequencing?

They lack the 3′-OH needed to add the next nucleotide. Normal DNA nucleotides already lack a 2′-OH, so absence of that group is not the chain-termination cause.

What is the canonical PAM for commonly used SpCas9, and what does it do?

The DNA motif 5′-NGG-3′, with N any base, lies next to the guide-matched target. PAM recognition helps SpCas9 bind and cleave DNA; PAM requirements differ among Cas proteins and variants.

What does degeneracy of the standard genetic code mean?

Different codons can specify the same amino acid; for example, six codons specify leucine. Degeneracy does not mean that each codon ordinarily specifies several amino acids.

Does reverse transcription violate Crick's original central dogma?

No. The usual expression pathway is DNA → RNA → protein, while reverse transcriptase copies RNA into DNA. Crick's dogma excludes transfer of sequence information from protein back to nucleic acid or into another protein sequence.

How can alternative splicing increase protein diversity from one gene?

Different splice-site choices and exon combinations can produce different mRNAs and protein isoforms. Not every splice product yields a stable, functional protein.

How does abundant charged tRNAᵀʳᵖ promote attenuation of the E. coli trp operon?

The ribosome translates the leader's Trp codons without stalling. This favors the 3–4 terminator hairpin rather than the 2–3 antiterminator, causing early transcription termination.

What catalyzes peptide-bond formation in the ribosome?

The large subunit's peptidyl-transferase center is an RNA-based catalyst: 23S rRNA in bacteria and 28S rRNA in human cytoplasmic ribosomes form its catalytic core.

What does wobble pairing allow during translation?

Flexible pairing between the codon's third base and the anticodon's first (5′) base lets one tRNA recognize more than one synonymous codon. Inosine can pair with U, C or A at this position.

What machinery removes most nuclear pre-mRNA introns, and what are their usual boundary dinucleotides?

The major spliceosome uses U1, U2, U4, U5 and U6 snRNPs. Most of its introns begin with 5′-GU and end with AG-3′; exceptions and a minor spliceosome exist.

How does a typical bacterial intrinsic transcription terminator work?

A GC-rich RNA hairpin followed by a U-rich tract promotes pausing and destabilization of the transcription complex, allowing RNA release without the Rho factor.

What are the repressor and physiological inducer of the E. coli lac operon?

LacI is the repressor that binds the operator. Allolactose, made from lactose by β-galactosidase, binds LacI and reduces its operator binding.

How can a eukaryotic enhancer increase transcription from a distant promoter?

Activator proteins bind this cis-regulatory DNA. Chromatin folding can bring enhancer-associated proteins near the promoter, with cofactors such as Mediator helping regulation; the mechanism is context dependent.

When does CAP–cAMP strongly activate the E. coli lac operon?

Low glucose generally raises cAMP, allowing CAP/CRP–cAMP to assist RNA polymerase recruitment. Strong transcription also requires relief of LacI repression, normally by allolactose; low glucose alone is insufficient.

How do histone acetyltransferases and deacetylases affect chromatin?

HATs add acetyl groups to lysines, neutralizing their positive charge and often favoring accessibility. HDACs remove these groups and often favor repression. Neither modification guarantees a particular gene's activity.

In the canonical animal miRNA pathway, which enzyme processes pre-miRNA after its export to the cytoplasm?

Dicer cuts the hairpin precursor into a short RNA duplex, usually about 21–23 nucleotides per strand. RNA interference uses small guide RNAs to reduce gene expression; not every miRNA follows this pathway.

Which RNA polymerase component recognizes the usual −10 and −35 promoter elements in E. coli?

The σ⁷⁰ sigma factor, which helps the bacterial RNA polymerase holoenzyme recognize these promoters.

What are the three stages of a typical Taq-based PCR cycle?

DNA denaturation at about 94–96°C, primer annealing often around 50–65°C, and extension around 72°C. Actual temperatures depend on the primers, enzyme and protocol.

Which standard-code stop codons trigger polypeptide release, and what recognizes them?

UAA, UAG and UGA are recognized by protein release factors at the ribosomal A site. They promote hydrolysis of the bond linking the polypeptide to its tRNA.

What does TBP recognize at a TATA-containing RNA polymerase II promoter?

The TATA box, often about 25–30 base pairs upstream of the start site. TBP is part of TFIID; not all polymerase II promoters contain a TATA box.

How do euchromatin and heterochromatin differ?

Euchromatin is generally less compact and more accessible; heterochromatin is more compact and usually repressive. Accessibility permits transcription but does not mean every gene is active.

What lariat linkage forms during spliceosomal splicing?

The intron's 5′ end joins the branch-point adenosine through a 2′–5′ phosphodiester bond, forming a branched lariat intermediate.

Why does DNA move toward the anode in agarose gels, and how are linear fragments separated?

DNA's phosphate backbone is negatively charged. Under usual conditions, smaller comparable linear DNA fragments migrate faster; conformation and gel conditions also affect migration.

How does tryptophan reduce transcription initiation at the E. coli trp operon?

Tryptophan acts as a corepressor: it binds TrpR, enabling the repressor to bind the operator and reduce transcription initiation.

Do all Type II restriction enzymes recognize palindromic sequences?

No. EcoRI recognizes the palindrome 5′-GAATTC-3′, read the same 5′→3′ on both strands. Type IIS enzymes are Type II enzymes that recognize asymmetric sequences and cut outside them.

Which protein tag can target a protein to the 26S proteasome?

Ubiquitin, attached through the E1–E2–E3 pathway. Appropriate polyubiquitin chains can signal proteasomal degradation; ubiquitination also has non-degradative functions.

Which three processing steps commonly mature an intron-containing eukaryotic pre-mRNA?

Addition of a 5′ 7-methylguanosine cap, intron removal with exon joining, and 3′ cleavage followed by poly(A)-tail addition. These are common pathways, not requirements for every transcript.

What do nuclear RNA polymerases I, II and III mainly transcribe in human cells?

I: a precursor of 18S, 5.8S and 28S rRNAs. II: protein-coding pre-mRNAs and many snRNAs. III: tRNAs, 5S rRNA and some other small RNAs.

How does guide-directed SpCas9 make a double-strand DNA break?

The guide RNA positions Cas9. Its HNH domain cuts the guide-complementary strand, and its RuvC domain cuts the other strand, typically near three base pairs upstream of the PAM.

Why does Taq polymerase support repeated PCR thermal cycles?

Its heat stability allows sufficient activity to remain after repeated brief high-temperature denaturation steps, avoiding enzyme replacement each cycle. It can still undergo thermal inactivation.

Molecular Biology, Gene Expression, Epigenetics & Biotechnology

32 advanced biochemistry and molecular-biology review cards on RNA transcription, pre-mRNA splicing and processing, aminoacyl-tRNA charging and ribosomal translation, prokaryotic operons, histone modification and DNA methylation, RNA interference, PCR, blotting, Sanger and next-generation sequencing, and CRISPR-Cas9.

Level: advanced
Languages: en → en
Cards: 32
Markdown: Molecular Biology, Gene Expression, Epigenetics & Biotechnology (.md)

Flashcards (32)

#	Front (Term / Question)	Back (Definition / Answer)
1	How can methylation of mammalian promoter CpG islands repress transcription?	It can recruit methyl-CpG-binding repressors and chromatin-modifying proteins, often reducing promoter accessibility and transcription. The effect depends on genomic and cellular context.
2	Which common bacterial ribosome-binding element helps position the start codon?	The Shine–Dalgarno sequence, often represented by the AGGAGG consensus, pairs with the 3′ end of 16S rRNA. Not all bacterial mRNAs use this element.
3	Which complex uses miRNA or siRNA guides to silence target mRNAs?	RISC, the RNA-induced silencing complex, contains an Argonaute protein that binds the guide. Silencing can involve RNA cleavage, decay or translational repression; not every Argonaute has slicing activity.
4	Why do ddNTPs terminate DNA synthesis in Sanger sequencing?	They lack the 3′-OH needed to add the next nucleotide. Normal DNA nucleotides already lack a 2′-OH, so absence of that group is not the chain-termination cause.
5	What is the canonical PAM for commonly used SpCas9, and what does it do?	The DNA motif 5′-NGG-3′, with N any base, lies next to the guide-matched target. PAM recognition helps SpCas9 bind and cleave DNA; PAM requirements differ among Cas proteins and variants.
6	What does degeneracy of the standard genetic code mean?	Different codons can specify the same amino acid; for example, six codons specify leucine. Degeneracy does not mean that each codon ordinarily specifies several amino acids.
7	Does reverse transcription violate Crick's original central dogma?	No. The usual expression pathway is DNA → RNA → protein, while reverse transcriptase copies RNA into DNA. Crick's dogma excludes transfer of sequence information from protein back to nucleic acid or into another protein sequence.
8	How can alternative splicing increase protein diversity from one gene?	Different splice-site choices and exon combinations can produce different mRNAs and protein isoforms. Not every splice product yields a stable, functional protein.
9	How does abundant charged tRNAᵀʳᵖ promote attenuation of the E. coli trp operon?	The ribosome translates the leader's Trp codons without stalling. This favors the 3–4 terminator hairpin rather than the 2–3 antiterminator, causing early transcription termination.
10	What catalyzes peptide-bond formation in the ribosome?	The large subunit's peptidyl-transferase center is an RNA-based catalyst: 23S rRNA in bacteria and 28S rRNA in human cytoplasmic ribosomes form its catalytic core.
11	What does wobble pairing allow during translation?	Flexible pairing between the codon's third base and the anticodon's first (5′) base lets one tRNA recognize more than one synonymous codon. Inosine can pair with U, C or A at this position.
12	What machinery removes most nuclear pre-mRNA introns, and what are their usual boundary dinucleotides?	The major spliceosome uses U1, U2, U4, U5 and U6 snRNPs. Most of its introns begin with 5′-GU and end with AG-3′; exceptions and a minor spliceosome exist.
13	How does a typical bacterial intrinsic transcription terminator work?	A GC-rich RNA hairpin followed by a U-rich tract promotes pausing and destabilization of the transcription complex, allowing RNA release without the Rho factor.
14	What are the repressor and physiological inducer of the E. coli lac operon?	LacI is the repressor that binds the operator. Allolactose, made from lactose by β-galactosidase, binds LacI and reduces its operator binding.
15	How can a eukaryotic enhancer increase transcription from a distant promoter?	Activator proteins bind this cis-regulatory DNA. Chromatin folding can bring enhancer-associated proteins near the promoter, with cofactors such as Mediator helping regulation; the mechanism is context dependent.
16	When does CAP–cAMP strongly activate the E. coli lac operon?	Low glucose generally raises cAMP, allowing CAP/CRP–cAMP to assist RNA polymerase recruitment. Strong transcription also requires relief of LacI repression, normally by allolactose; low glucose alone is insufficient.
17	How do histone acetyltransferases and deacetylases affect chromatin?	HATs add acetyl groups to lysines, neutralizing their positive charge and often favoring accessibility. HDACs remove these groups and often favor repression. Neither modification guarantees a particular gene's activity.
18	In the canonical animal miRNA pathway, which enzyme processes pre-miRNA after its export to the cytoplasm?	Dicer cuts the hairpin precursor into a short RNA duplex, usually about 21–23 nucleotides per strand. RNA interference uses small guide RNAs to reduce gene expression; not every miRNA follows this pathway.
19	Which RNA polymerase component recognizes the usual −10 and −35 promoter elements in E. coli?	The σ⁷⁰ sigma factor, which helps the bacterial RNA polymerase holoenzyme recognize these promoters.
20	What are the three stages of a typical Taq-based PCR cycle?	DNA denaturation at about 94–96°C, primer annealing often around 50–65°C, and extension around 72°C. Actual temperatures depend on the primers, enzyme and protocol.
21	Which standard-code stop codons trigger polypeptide release, and what recognizes them?	UAA, UAG and UGA are recognized by protein release factors at the ribosomal A site. They promote hydrolysis of the bond linking the polypeptide to its tRNA.
22	What does TBP recognize at a TATA-containing RNA polymerase II promoter?	The TATA box, often about 25–30 base pairs upstream of the start site. TBP is part of TFIID; not all polymerase II promoters contain a TATA box.
23	How do euchromatin and heterochromatin differ?	Euchromatin is generally less compact and more accessible; heterochromatin is more compact and usually repressive. Accessibility permits transcription but does not mean every gene is active.
24	What lariat linkage forms during spliceosomal splicing?	The intron's 5′ end joins the branch-point adenosine through a 2′–5′ phosphodiester bond, forming a branched lariat intermediate.
25	Why does DNA move toward the anode in agarose gels, and how are linear fragments separated?	DNA's phosphate backbone is negatively charged. Under usual conditions, smaller comparable linear DNA fragments migrate faster; conformation and gel conditions also affect migration.
26	How does tryptophan reduce transcription initiation at the E. coli trp operon?	Tryptophan acts as a corepressor: it binds TrpR, enabling the repressor to bind the operator and reduce transcription initiation.
27	Do all Type II restriction enzymes recognize palindromic sequences?	No. EcoRI recognizes the palindrome 5′-GAATTC-3′, read the same 5′→3′ on both strands. Type IIS enzymes are Type II enzymes that recognize asymmetric sequences and cut outside them.
28	Which protein tag can target a protein to the 26S proteasome?	Ubiquitin, attached through the E1–E2–E3 pathway. Appropriate polyubiquitin chains can signal proteasomal degradation; ubiquitination also has non-degradative functions.
29	Which three processing steps commonly mature an intron-containing eukaryotic pre-mRNA?	Addition of a 5′ 7-methylguanosine cap, intron removal with exon joining, and 3′ cleavage followed by poly(A)-tail addition. These are common pathways, not requirements for every transcript.
30	What do nuclear RNA polymerases I, II and III mainly transcribe in human cells?	I: a precursor of 18S, 5.8S and 28S rRNAs. II: protein-coding pre-mRNAs and many snRNAs. III: tRNAs, 5S rRNA and some other small RNAs.
31	How does guide-directed SpCas9 make a double-strand DNA break?	The guide RNA positions Cas9. Its HNH domain cuts the guide-complementary strand, and its RuvC domain cuts the other strand, typically near three base pairs upstream of the PAM.
32	Why does Taq polymerase support repeated PCR thermal cycles?	Its heat stability allows sufficient activity to remain after repeated brief high-temperature denaturation steps, avoiding enzyme replacement each cycle. It can still undergo thermal inactivation.