Textbook Reading Week 1

DNA Transcription

The process of copying a specific portion of DNA (a gene) into a complementary RNA sequence. This is the first step in gene expression.

RNA Translation

The process where the RNA sequence is used as a template to direct the synthesis of a protein. This occurs on ribosomes.

Central Dogma of Molecular Biology

The fundamental principle that genetic information flows from DNA to RNA to protein. This flow is universal in all living cells.

RNA Splicing

A processing step in eukaryotic cells where introns (non-coding sequences) are removed from the primary RNA transcript and exons (coding sequences) are joined together. This occurs in the nucleus.

Transcription Unit

1. A segment of DNA that is transcribed into a single RNA molecule.

2. In eukaryotes, it typically contains one gene; in bacteria, it can contain multiple adjacent genes.

Transcription Unit 1

A segment of DNA that is transcribed into a single RNA molecule.

Transcription Unit 2

In eukaryotes, it typically contains one gene; in bacteria, it can contain multiple adjacent genes.

RNA Polymerase

1. The enzyme that catalyzes transcription by synthesizing an RNA chain complementary to a DNA template strand.

2. It uses ribonucleotide triphosphates (ATP, UTP, CTP, GTP) as substrates.

RNA Polymerase 1

1. The enzyme that catalyzes transcription by synthesizing an RNA chain complementary to a DNA template strand.

RNA Polymerase 2

It uses ribonucleotide triphosphates (ATP, UTP, CTP, GTP) as substrate

RNA Polymerase Holoenzyme (Bacteria)

1. The functional bacterial RNA polymerase complex

2. consisting of the core enzyme plus a sigma (σ) factor

3. The σ factor helps the enzyme recognize and bind to promoter sequences.

RNA Polymerase Holoenzyme (Bacteria) 1

The functional bacterial RNA polymerase complex

RNA Polymerase Holoenzyme (Bacteria) 2

consisting of the core enzyme plus a sigma (σ) factor

RNA Polymerase Holoenzyme (Bacteria) 3

The σ factor helps the enzyme recognize and bind to promoter sequences.

Promoter

1. A specific DNA sequence that signals the start point for transcription.

2. RNA polymerase binds tightly to the promoter to initiate RNA synthesis.

Promoter 1

A specific DNA sequence that signals the start point for transcription.

Promoter 2

RNA polymerase binds tightly to the promoter to initiate RNA synthesis.

Sigma (σ) Factor

1. bacterial transcription initiation factor

2. associates with the RNA polymerase core enzyme to form the holoenzyme

3. It recognizes and binds to promoter sequences in DNA.

Sigma (σ) Factor 1

bacterial transcription initiation factor

Sigma (σ) Factor 2

associates with the RNA polymerase core enzyme to form the holoenzyme

Sigma (σ) Factor 3

It recognizes and binds to promoter sequences in DNA.

Transcription Bubble

1. A region of approximately 10 nucleotides of unpaired DNA that

2. formed when RNA polymerase unwinds the DNA double helix at the transcription start site.

Transcription Bubble 1

A region of approximately 10 nucleotides of unpaired DNA that

Transcription Bubble 2

formed when RNA polymerase unwinds the DNA double helix at the transcription start site.

Terminator

A DNA sequence that signals RNA polymerase to stop transcription and release the newly synthesized RNA transcript and the DNA template.

Consensus Sequence

1. A summary sequence derived from comparing many sequences with the same function (e.g., promoters)

2. It represents the most common nucleotide found at each position.

Consensus Sequence 1

A summary sequence derived from comparing many sequences with the same function (e.g., promoters)

Consensus Sequence 2

It represents the most common nucleotide found at each position.

Sequence Logo

1. A graphical representation of the consensus sequence that shows the relative frequency of each nucleotide at each position

2. with the total height indicating the information content.

Sequence Logo 1

1. A graphical representation of the consensus sequence

2. shows the relative frequency of each nucleotide at each position

Sequence Logo 2

with the total height indicating the information content.

General Transcription Factors

1. A set of proteins required for the initiation of transcription by eukaryotic RNA polymerase II.

2. They help position the polymerase, unwind DNA, and initiate transcription.

3. Examples include TFIID, TFIIB, TFIIH.

General Transcription Factors 1

A set of proteins required for the initiation of transcription by eukaryotic RNA polymerase II.

General Transcription Factors 2

They help position the polymerase, unwind DNA, and initiate transcription.

General Transcription Factors 3

Examples include TFIID, TFIIB, TFIIH.

TATA Box

1. A common promoter element in eukaryotes, with the consensus sequence TATAAA,

2. located about 25 nucleotides upstream of the transcription start site

3. It is recognized by the TBP subunit of TFIID.

TATA Box 1

A common promoter element in eukaryotes, with the consensus sequence TATAAA,

TATA Box 2

located about 25 nucleotides upstream of the transcription start site

TATA Box 3

It is recognized by the TBP subunit of TFIID.

TBP (TATA-Binding Protein)

1. A subunit of the general transcription factor TFIID that binds to the TATA box

2. causing a significant bend in the DNA

3. which serves as a landmark for the assembly of other transcription factors.

TBP (TATA-Binding Protein) 1

A subunit of the general transcription factor TFIID that binds to the TATA box

TBP (TATA-Binding Protein) 2

causing a significant bend in the DNA

TBP (TATA-Binding Protein) 3

which serves as a landmark for the assembly of other transcription factors.

TFIIH

1. large, multi-subunit general transcription factor in eukaryotes.

2. contains DNA helicase and protein kinase activities.

3. unwinds DNA at the start site

4. phosphorylates the C-terminal domain (CTD) of RNA polymerase II.

TFIIH 1

large, multi-subunit general transcription factor in eukaryotes.

TFIIH 2

contains DNA helicase and protein kinase activities.

TFIIH 3

unwinds DNA at the start site

TFIIH 4

phosphorylates the C-terminal domain (CTD) of RNA polymerase II.

CTD (C-Terminal Domain)

1. The long tail of RNA polymerase II,

2. consisting of multiple tandem repeats of a 7-amino acid sequence.

3. Phosphorylation of serines in the CTD helps release the polymerase from the initiation complex and recruits RNA processing enzymes.

CTD (C-Terminal Domain) 1

The long tail of RNA polymerase II,

CTD (C-Terminal Domain) 2

consisting of multiple tandem repeats of a 7-amino acid sequence.

CTD (C-Terminal Domain) 3

phosphorylation of serines in CTD helps release polymerase from initiation complex and recruits RNA processing enzymes.

Mediator

A large protein complex in eukaryotes that acts as a bridge between transcription activator proteins (bound to enhancers) and RNA polymerase II with the general transcription factors at the promoter. It helps regulate transcription initiation.

Mediator 1

A large protein complex in eukaryotes

Mediator 2

acts as bridge between transcription activator proteins (bound to enhancers) and RNA polymerase II with general transcription factors at promoter.

Mediator 3

It helps regulate transcription initiation.

Transcriptional Activators

Gene regulatory proteins that bind to specific DNA sequences (enhancers) and help recruit RNA polymerase II and the general transcription machinery to the promoter to initiate transcription.

Transcriptional Activators 1

Gene regulatory proteins that bind to specific DNA sequences (enhancers)

While they can bind directly to the promoter region, they most often bind to enhancers

Transcriptional Activators 2

help recruit RNA polymerase II and general transcription machinery to promoter to initiate transcription.

Chromatin Remodeling Complexes

1. ATP-dependent enzyme complexes that alter the structure of nucleosomes to make DNA more accessible for transcription.

2. They are recruited by activators to promoters.

Chromatin Remodeling Complexes 1

ATP-dependent enzyme complexes that alter structure of nucleosomes to make DNA more accessible for transcription.

Chromatin Remodeling Complexes 2

They are recruited by activators to promoters.

Histone-Modifying Enzymes

Enzymes that add or remove chemical groups (e.g., acetyl, methyl) from histones. These modifications can make chromatin more open and accessible for transcription.

Histone-Modifying Enzymes 1

Enzymes that add or remove chemical groups (e.g., acetyl, methyl) from histones.

Histone-Modifying Enzymes 2

These modifications can make chromatin more open and accessible for transcription.

Elongation Factors

Proteins that associate with RNA polymerase during transcription elongation to increase its processivity and help it move through various DNA sequences and chromatin structures.

DNA Supercoiling

1. A conformational state of DNA that occurs in response to helical tension.

2. RNA polymerase generates positive supercoiling ahead of it and negative supercoiling behind it as it moves along anchored DNA.

DNA Supercoiling 1

A conformational state of DNA that occurs in response to helical tension.

DNA Supercoiling 2

RNA polymerase generates positive supercoiling ahead of it and negative supercoiling behind it as it moves along anchored DNA.

Topoisomerases

Enzymes that relieve superhelical tension in DNA by creating transient breaks in the DNA backbone. They allow DNA strands to swivel around each other.

Primary Transcript (pre-mRNA)

The initial RNA molecule synthesized by RNA polymerase II. It contains both introns and exons and undergoes processing (capping, splicing, polyadenylation) to become mature mRNA.

5' Cap

A modified guanine nucleotide added to the 5' end of a eukaryotic pre-mRNA shortly after transcription initiation. It protects the RNA from degradation and is recognized by the translation machinery.

Introns

Non-coding sequences within a gene that are transcribed into RNA but are removed by splicing before the RNA becomes functional.

Exons

Coding sequences within a gene that are retained in the mature mRNA after splicing and specify the amino acid sequence of a protein.

Spliceosome

A large, dynamic complex of five snRNPs and numerous additional proteins that catalyzes the removal of introns and the joining of exons in eukaryotic pre-mRNA.

snRNPs

1. (small nuclear ribonucleoproteins)

2. Complexes of snRNA and proteins that are key components of the spliceosome.

3. They recognize splice sites and catalyze the splicing reactions.

Transesterification Reactions

1. two-step biochemical reactions catalyzed by spliceosome.

2. first reaction involves attack by 2' OH of specific adenosine (branch point) on 5' splice site.

3. second reaction joins exons.

Transesterification Reactions 1

two-step biochemical reactions catalyzed by spliceosome.

Transesterification Reactions 2

first reaction involves attack by 2' OH of specific adenosine (branch point) on 5' splice site.

Transesterification Reactions 3

second reaction joins exons

Lariat Intermediate

branched, looped structure formed during RNA splicing when 5' end of intron is covalently linked to adenosine (branch point) within intron.

Lariat Intermediate 1

branched, looped structure formed during RNA splicing

Lariat Intermediate 2

when 5' end of intron is covalently linked to adenosine (branch point) within intron

Alternative Splicing

A process where different combinations of exons are joined together from the same primary transcript. This allows a single gene to produce multiple different protein isoforms.

CsF

1. (Cleavage Stimulation Factor)

2. A protein complex

3. binds to GU-rich / U-rich element downstream of cleavage site in pre-mRNA

4. involved in forming 3' end of eukaryotic mRNA.

CsF (Cleavage Stimulation Factor) 1

protein complex

CsF (Cleavage Stimulation Factor) 2

binds to GU-rich / U-rich element downstream of cleavage site in pre-mRNA

CsF (Cleavage Stimulation Factor) 3

involved in forming 3' end of eukaryotic mRNA.

CPSF

(Cleavage and Polyadenylation Specificity Factor)

A protein complex that binds to the AAUAAA sequence in the pre-mRNA and is involved in the cleavage and polyadenylation reactions that form the 3' end of eukaryotic mRNA.

CPSF 1

(Cleavage and Polyadenylation Specificity Factor)

A protein complex that binds to the AAUAAA sequence in the pre-mRNA

CPSF 2

is involved in the cleavage and polyadenylation reactions that form the 3' end of eukaryotic mRNA.

Poly-A Polymerase (PAP)

An enzyme that adds a series of adenine nucleotides (the poly-A tail) to the 3' end of a cleaved eukaryotic mRNA. It does not require a template.

(PAP) 1

Poly-A Polymerase

An enzyme that adds series of adenine nucleotides (poly-A tail) to 3' end of cleaved eukaryotic mRNA.

(PAP) 2

Poly-A Polymerase

does not require template

Poly-A Tail

A sequence of approximately 200 adenine nucleotides added to the 3' end of a eukaryotic mRNA after cleavage. It protects the mRNA from degradation and aids in translation and export from the nucleus.

Poly-A-Binding Proteins

Proteins that bind to the poly-A tail of an mRNA. They help determine the tail's length and protect the mRNA from degradation.

mRNA Export

The process by which mature, fully processed mRNA molecules are selectively transported from the nucleus to the cytoplasm for translation. It is signaled by the presence of specific proteins (cap-binding, exon junction, poly-A-binding) and the absence of proteins signifying incomplete processing.

mRNA Export 1

process which mature, fully processed mRNA molecules are selectively transported from nucleus to cytoplasm for translation.

mRNA Export 2

signaled by presence of specific proteins (cap-binding, exon junction, poly-A-binding) and absence of proteins signifying incomplete processing.

RNA World Hypothesis

The theory that early life forms used RNA both to store genetic information and to catalyze chemical reactions, before the evolution of DNA and proteins. Self-splicing introns are considered molecular fossils from this RNA world.