Genetics Chapter 13: Transcription

1. living organisms must be able to store and faithfully transmit genetic information during reproduction

2. organisms must have the ability to catalyze the chemical transformations that drive life processes

what are the two basic functions required by life?

biological catalyst

Thomas Cech and his colleagues discovered that RNA can serve as a ___ ___

catalytic RNA molecules that can cut out parts of their own sequences, connect some RNA molecules together, replicate others, and catalyze the formation of peptide bonds between amino acids

what are ribozymes?

genetic instructions for protein production

what does mRNA carry?

enzyme and genetic material

RNA is thought to be the first ...

ribonucleotides

RNA is a polymer of ___

adenine, guanine, cytosine, and uracil

what are the ribonucleotides that make up RNA?

RNA

which is less stable- RNA or DNA?

due to the hydroxyl at the 2' position on the ribose sugar (extra O)

why is RNA less stable than DNA?

the sequence of nucleotides

what is the RNA primary structure?

1. RNA contains ribose, DNA contains deoxyribose

2. uracil replaces thymine in RNA

3. RNA is usually single stranded while DNA is normally double stranded

what are the main differences between DNA and RNA?

stable folding into stem/loop and other structures

how is RNA secondary structure produced?

the sequence of the nucleotides and how they interact

what is secondary structure of RNA determined by?

structural and functional components of the ribosome

what is the function of ribosomal RNA (rRNA)?

carries genetic code for proteins

what is the function of messenger RNA (mRNA)?

helps incorporate amino acids into polypeptide chain

what is the function of transfer RNA?

precursor to mRNA, has introns before splicing occurs

what is the function of pre-messenger RNA (pre-mRNA)?

processing of pre-mRNA, part of splicing machinery

what is the function of small nuclear RNA (snRNA)?

processing and assembly of rRNA

what is the function of small nucleolar RNA (snoRNA)?

inhibits translation of mRNA

what is the function of microRNA (miRNA)?

triggers degradation of other RNA molecules

what is the function of small interfering RNA (siRNA)?

suppresses the transcription of transposable elements in reproductive cells

what is the function of Piwi-interacting RNAs (piRNAs)?

assists in destruction of foreign DNA in prokaryotic cells

what is the function of CRISPR RNA (crRNA)?

by transcription from DNA templates

how are all cellular RNAs synthesized?

cytoplasm

what is the location of ribosomal RNA in eukaryotic cells?

nucleus and cytoplasm

what is the location of messenger RNA in eukaryotic cells?

cytoplasm

what is the location of transfer RNA in eukaryotic cells?

nucleus

what is the location of pre-messenger RNA in eukaryotic cells?

ribonucleotide triphosphates

what are the substrates for the synthesis of RNA?

RNA polymerase enzymes

what catalyzes RNA synthesis?

mRNA, rRNA, tRNA

what RNAs are common to both prokaryotes and eukaryotes?

transcription

what do Christmas tree-like structures indicate?

a DNA molecule

what is the "trunk" in a Christmas tree structure?

what are the "branches" in a Christmas tree structure?

on side of "branch" closest to "trunk"

where is the 3' end of RNA in a Christmas tree structure?

at the tip of the "branch," furthest from the trunk

where is the 5' end of RNA in a Christmas tree structure?

promoter

all RNA polymerases begin at the ___

the RNA strand produced gets longer

what happens as an RNA polymerase progresses further down the "trunk" in a Christmas tree structure?

RNA polymerase

each RNA strand in a Christmas tree structure has its own ___ ___

1. a DNA template

2. the raw materials (ribonucleotide triphosphates) needed to build a new RNA molecule

3. the transcription apparatus, consisting of the proteins necessary for catalyzing the synthesis of RNA

what are the 3 major components required for transcription?

complementary, antiparallel

RNA synthesis is ___ and ___ to the template strand

a single strand of the DNA double helix

what is the template strand for RNA synthesis?

transcription takes place on only one of the two nucleotide strands, there is a template and nontemplate strand

what is different about the template strand in RNA synthesis compared to DNA replication?

to the 3'-OH group

where are new nucleotides added in RNA synthesis?

5'-->3' (of the growing RNA)

what direction does transcription proceed?

the promoter

how is the direction of transcription (if top or bottom strand is used) determined?

one direction

individual genes are transcribed in ___ ___

either direction

different genes can be described in ___ ___

a stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription

what is the transcription unit?

1. promoter

2. RNA-coding region

3. terminator

what are the 3 regions of the transcription unit?

a DNA sequence that the transcription apparatus recognizes and binds

what is a promoter?

which of the two DNA strands is to be read as the template, the direction of transcription, an dthe transcription start site

what does the promoter indicate?

next to the transcription start site (but is not itself transcribed)

where is the promoter usually located?

a sequence of DNA nucleotides that is copied into an RNA molecule

what is the RNA-coding region?

a sequence of nucleotides that signals where transcription is to end (usually part of the RNA-coding sequence)

what is the terminator?

a ribose sugar and a base attached to 3 phosphate groups

what are ribonucleotide triphosphates made of?

a transcription bubble

what does the initiation of transcription produce?

primer

initiation of RNA synthesis does not require a ___

one

how many types of RNA polymerase do bacterial cells usually possess?

alpha, beta, beta prime, and omega subunits

what is bacterial RNA polymerase composed of?

controls binding of bacterial RNA polymerase to the promoter

what does the sigma factor do?

1. initiation

2. elongation

3. termination

what are the steps of bacterial transcription?

transcription apparatus assembles at the promoter and begins RNA synthesis

what happens during initiation in bacterial transcription?

progressive addition of nucleotides at the 3'-hydroxyl by RNA polymerase

what happens during elongation in bacterial transcription?

recognition of the end of the transcription unit and dissociating the polymerase and transcript

what happens during termination in bacterial transcription?

1. promoter recognition

2. transcription bubble formation

3. first nucleotide bonds formed

4. polymerase escape from the promoter region

what are the steps of bacterial initiation?

the set of the most commonly encountered nucleotides among sequences that possess considerable similarity

what are consensus sequences?

-10 consensus sequence

what is the most commonly encountered consensus sequence, found in almost all bacterial promoters?

centered about 10 bp upstream of the start site, written as TATAAT

what is the -10 consensus sequence?

lies 35 nucleotides upstream of start site, common to most bacterial promoters, TTGACA

what is the -35 consensus sequence?

joins the other subunits and forms the holoenzyme

what does the sigma factor do in bacterial initiation?

at the transcription initiation site

where is the holoenzyme positioned in bacterial initiation?

undergoes a conformational change, causes tight binding and formation of the transcription bubble

what does the holoenzyme do in bacterial initiation?

RNA polymerase is positioned over the transcription start site (at position +1) and unwinds the DNA to produce a single-stranded template

what happens in bacterial transcription once the holoenzyme has bound to the promoter?

locations of the consensus sequences

what is the position of the start site determined by?

pyrophosphate (2 phosphate groups) and sigma factor is released, polymerase moves beyond the promoter

what happens as new nucleotides are added in bacterial initiation?

processive

RNA polymerase is highly ___

moves forward quickly and moves the transcription bubble as transcription proceeds

RNA polymerase is highly processive, meaning it ...

RNA polymerase undergoes a change in its conformation and is no longer able to bind to the consensus sequences in the promoter, allows it to escape from the promoter and begin transcribing downstream

what happens at the end of initiation?

RNA polymerase can pause and backtrack

what allows for proofreading in bacterial RNA synthesis?

by recognition of a rho utilization (Rut) site

how does Rho-dependent termination occur?

Rho-dependent terminators and Rho-independent terminators

what are the two major types of terminators in bacterial cells?

Rho binds to RNA and moves to the 3' end, when the Rho protein reaches the 3' end it dissociates the polymerase and transcription

describe what happens during Rho-dependent termination

Rho-independent termination

what is the about 50% of the termination in prokaryotes?

an inverted repeat sequence forms a hairpin loop, this conformation change causes a stretch of A-U (weaker) base pairs to dissociate the transcript

what happens during Rho-independent termination?

I, II, II

what RNA polymerases are found in all eukaryotes?

IV, V

what RNA polymerases are found in plants?

large rRNAs

what does RNA polymerase I transcribe?

pre-mRNAs, snRNAs, some miRNAs, some snRNAs

what does RNA polymerase II transcribe?

tRNAs, small rRNAs, some miRNAs, some snRNAs

what does RNA polymerase III transcribe?

siRNAs that silence transposons

what does RNA polymerase IV transcribe?

siRNAs that affect chromatin

what does RNA polymerase V transcribe?

both go through initiation, elongation, and termination

what is a similarity between eukaryotic and prokaryotic transcription?

eukaryotic transcription is regulated by changes in chromatin structure while prokaryotic is not, different consensus sequences, different protein factors

what are some differences between eukaryotic and prokaryotic transcription?

the core promoter and the regulatory promoter

what are the two primary parts of a promoter for a gene transcribed by RNA polymerase II?

located immediately upstream of the gene, site to which the basal transcription apparatus binds

what is the core promoter?

consensus sequences

the core promoter typically includes one or more ___ ___

the TATA box

what is the most common consensus sequence a core promoter can contain?

are recognized by certain transcription factors, which bind to them and serve as a platform for the assembly of the basal transcription apparatus

what doe consensus sequences in the core promoter do?

located immediately upstream of the core promoter, can contain a variety of consensu sequences

what is the regulatory promoter?