ch 13 genetics

Explain how the structure of RNA allows it to participate in a variety of cellular functions.

RNA, or ribonucleic acid, is a single-stranded molecule composed of nucleotides that contain ribose sugar, a phosphate group, and nitrogenous bases. Its versatile structure allows it to fold into various shapes, enabling it to play essential roles in protein synthesis, gene regulation, and as genomic material for some viruses.

RNA structure and early life

Early life used RNA both as the carrier of genetic information and as a biological catalyst.

RNA basic structure

A polymer consisting of nucleotides joined by phosphodiester bonds; contains ribose sugar, a phosphate group, and uracil (instead of thymine); usually single-stranded and can form secondary structures.

Ribosomal RNA (rRNA) general function

A component of the ribosome that helps carry out translation.

Messenger RNA (mRNA) general function

Carries coding instructions for proteins from DNA to the ribosome.

Transfer RNA (tRNA) general function

Helps incorporate amino acids into a polypeptide chain during translation.

Describe the major components required for transcription.

1) DNA Template Strand (3' to 5' strand containing promoter, RNA-coding region, and terminator); 2) Substrates (rNTPs: ATP, CTP, GTP, UTP; requires no primer); 3) RNA Polymerase (Prokaryotic core + sigma factor OR Eukaryotic Pol I, II, III); 4) Transcription Factors (GTFs, activators, and chromatin remodelers).

Transcription template

Single-stranded DNA; synthesis is complementary and antiparallel to the DNA template strand.

Transcription unit components

Promoter, RNA-coding region, and terminator.

Transcription substrates

Ribonucleoside triphosphates (rNTPs: ATP, GTP, CTP, UTP).

Bacterial RNA polymerase structure

Consists of a core enzyme (catalyzes nucleotide addition) and a sigma factor (controls promoter binding).

Eukaryotic RNA polymerases

Eukaryotic cells contain multiple distinct types of RNA polymerases (RNA Pol I, II, III, IV, and V).

Outline the process of bacterial transcription

Process of Bacterial Transcription (Overview)---Consists of three main stages: 1) Initiation (promoter binding by sigma factor and DNA unwinding), 2) Elongation (5' to 3' RNA synthesis by core enzyme), and 3) Termination (transcript release via Rho-dependent or Rho-independent mechanisms).

Bacterial Transcription Stage 1: Initiation---Sigma factor recognizes -10 (Pribnow box) and -35 promoter sequences, directing the core enzyme to form the holoenzyme; DNA unwinds to form an open complex, short initial RNAs are made (abortive initiation), and sigma factor is released.

Bacterial Transcription Stage 2: Elongation---RNA polymerase core enzyme moves 3' to 5' along the DNA template strand, unwinding DNA and synthesizing complementary RNA 5' to 3' using rNTPs within a moving transcription bubble.

Bacterial Transcription Stage 3: Termination---Transcription ceases after a terminator sequence is transcribed, destabilizing the RNA-DNA hybrid and releasing the completed RNA transcript and core enzyme.

Rho-Independent Termination (Intrinsic)---Termination mechanism where an transcribed inverted repeat forms an RNA hairpin loop followed by a poly-U tract, destabilizing base pairing and releasing the transcript without protein assistance.

Rho-Dependent Termination---Termination mechanism where Rho factor (a helicase protein) binds to the C-rich rut site on RNA, moves toward the 3' end, and unwinds the RNA-DNA hybrid when RNA polymerase pauses at the terminator.

Stages of transcription

Initiation, elongation, and termination.

Bacterial transcription initiation

Begins at the start site determined by consensus sequences in a promoter; DNA unwinds near the start site to form a transcription bubble.

Bacterial transcription termination

Occurs after a terminator sequence is transcribed; uses either rho-dependent or rho-independent terminators.

compare and contrast transcription in bacteria and eukaryotes

Process of Bacterial Transcription (Overview)---Consists of three main stages: 1) Initiation (promoter binding by sigma factor and DNA unwinding), 2) Elongation (5' to 3' RNA synthesis by core enzyme), and 3) Termination (transcript release via Rho-dependent or Rho-independent mechanisms).

Bacterial Transcription Stage 1: Initiation---Sigma factor recognizes -10 (Pribnow box) and -35 promoter sequences, directing the core enzyme to form the holoenzyme; DNA unwinds to form an open complex, short initial RNAs are made (abortive initiation), and sigma factor is released.

Bacterial Transcription Stage 2: Elongation---RNA polymerase core enzyme moves 3' to 5' along the DNA template strand, unwinding DNA and synthesizing complementary RNA 5' to 3' using rNTPs within a moving transcription bubble.

Bacterial Transcription Stage 3: Termination---Transcription ceases after a terminator sequence is transcribed, destabilizing the RNA-DNA hybrid and releasing the completed RNA transcript and core enzyme.

Rho-Independent Termination (Intrinsic)---Termination mechanism where an transcribed inverted repeat forms an RNA hairpin loop followed by a poly-U tract, destabilizing base pairing and releasing the transcript without protein assistance.

Rho-Dependent Termination---Termination mechanism where Rho factor (a helicase protein) binds to the C-rich rut site on RNA, moves toward the 3' end, and unwinds the RNA-DNA hybrid when RNA polymerase pauses at the terminator.

Eukaryotic transcription initiation

Requires modification of chromatin structure; general transcription factors bind the core promoter, while activators bind regulatory promoters/enhancers.

Section 13.5 Learning Objective

Compare transcription in archaea to that in bacteria and eukaryotes.

Archaeal transcription

Has many similarities to eukaryotic transcription, including similar RNA polymerases, promoters, and transcription factors.

ribozyme

An RNA molecule capable of acting as a biological catalyst.

ribosomal RNA (rRNA)

RNA component of the ribosome; conducts translation and peptide bond formation.

messenger RNA (mRNA)

Protein-coding RNA transcript that carries genetic information from DNA to the ribosome.

pre-messenger RNA (pre-mRNA)

Primary eukaryotic RNA transcript containing introns and exons that must undergo processing to become mature mRNA.

transfer RNA (tRNA)

Adaptor RNA that carries a specific amino acid to the ribosome during translation.

small nuclear RNA (snRNA)

Small RNA found in the nucleus that processes pre-mRNA by forming part of the spliceosome.

small nuclear ribonucleoprotein (snRNP)

Complex of snRNA and proteins involved in pre-mRNA splicing.

small nucleolar RNA (snoRNA)

Small RNA that guides chemical modifications and processing of rRNA in the nucleolus.

microRNA (miRNA)

Small single-stranded regulatory RNA (~21–22 nt) that represses translation or triggers mRNA degradation.

small interfering RNA (siRNA)

Small double-stranded regulatory RNA (~21–25 nt) that degrades complementary target mRNA through RNA interference.

Piwi-interacting RNA (piRNA)

Small RNA that combines with Piwi proteins to suppress transposable element movement in germline cells.

long noncoding RNA (lncRNA)

Noncoding RNA transcript longer than 200 nucleotides that regulates gene expression, chromatin structure, or transcription.

CRISPR RNA (crRNA)

Small prokaryotic RNA derived from foreign viral sequences that directs Cas nucleases to cleave foreign nucleic acids.

template strand

The 3' to 5' DNA strand used by RNA polymerase to synthesize complementary RNA.

nontemplate strand

The 5' to 3' DNA strand complementary to the template strand; matches the sequence of the synthesized RNA (except T instead of U).

transcription unit

A stretch of DNA containing a promoter, RNA-coding region, and terminator required to yield an RNA transcript.

promoter

DNA sequence recognized and bound by transcription machinery to set the transcription start site and direction.

RNA-coding region

The sequence of DNA nucleotides that is copied into an RNA molecule.

terminator

DNA sequence that signals the end of transcription and promotes transcript release.

ribonucleoside triphosphate (rNTP)

Substrate for RNA synthesis consisting of a ribose sugar, a nitrogenous base, and three phosphate groups.

RNA polymerase

Enzyme that catalyzes 5' to 3' RNA synthesis using a DNA template.

core enzyme

Bacterial RNA polymerase complex responsible for elongation, lacking promoter recognition capability without the sigma factor.

sigma (σ) factor

Bacterial protein subunit that directs core RNA polymerase to bind specifically to promoters.

holoenzyme

Functional bacterial complex consisting of the core RNA polymerase enzyme plus the sigma factor.

RNA polymerase I

Eukaryotic enzyme that transcribes large ribosomal RNAs (28S, 18S, 5.8S).

RNA polymerase II

Eukaryotic enzyme that transcribes pre-mRNAs, snRNAs, miRNAs, and lncRNAs.

RNA polymerase III

Eukaryotic enzyme that transcribes tRNAs, 5S rRNA, and small nuclear RNAs.

RNA polymerase IV

Plant-specific enzyme involved in RNA-directed DNA methylation and siRNA generation.

RNA polymerase V

Plant-specific enzyme involved in heterochromatin formation and transcript-guided gene silencing.

consensus sequence

The set of most common nucleotides found across homologous DNA or RNA regulatory sequences.

−10 consensus sequence (Pribnow box)

Bacterial promoter motif (5'-TATAAT-3') located ~10 bp upstream of start site; aids in DNA unwinding.

−35 consensus sequence

Bacterial promoter motif (5'-TTGACA-3') located ~35 bp upstream of start site; recognized by the sigma factor.

upstream element

AT-rich sequence located ~-40 to -60 in some bacterial promoters that increases transcription rate.

abortive initiation

Release of short RNA transcripts (2 to 10 nt) before RNA polymerase clears the promoter and enters processive elongation.

rho-dependent terminator

Bacterial termination site requiring the Rho protein factor to release the RNA transcript.

rho factor (ρ)

ATP-dependent helicase protein that binds RNA at the rut site and unwinds the RNA-DNA hybrid to terminate transcription.

rho-independent terminator

Sequence forming an RNA hairpin followed by a poly-U tract, causing spontaneous termination.

polycistronic mRNA

Single prokaryotic mRNA molecule containing coding sequences for multiple structural genes in an operon.

transcription factor

Protein that binds to DNA or other proteins to regulate the initiation rate of transcription.

general transcription factor

Essential eukaryotic protein that binds to core promoters with RNA Pol II to establish baseline transcription.

basal transcription apparatus

Complex composed of RNA polymerase II, general transcription factors, and Mediator assembled at the core promoter.

core promoter

Minimal promoter site adjacent to the start site where the basal transcription apparatus assembles.

TATA box

Consensus sequence (5'-TATAAA-3') in eukaryotic core promoters located ~-25 to -30 bp upstream of initiation.

regulatory promoter

Region upstream of core promoter containing binding sites for transcriptional activator proteins.

enhancer

Distal DNA regulatory element that binds activators to boost transcription from a distant promoter.

internal promoter

Promoter sequence positioned downstream of the transcription start site within the coding region (typical for RNA Pol III).

TATA-binding protein (TBP)

Subunit of TFIID that binds directly to the TATA box, causing a bend in DNA that aids pre-initiation complex assembly.