Genetics Chapter 13

replication

the mechanism by which new DNA molecules are synthesized using single-stranded DNA templates in a semiconservative manner

transcription

uses the coding instructions in DNA to create the traits of an organism, through coping DNA sequences into RNA

How are replication and transcription similar?

- both require the reading DNA polynucleotide strands
- both move in 5' to 3' direction

How are replication and transcription different?

- replication requires DNA polymerase, while transcription requires RNA polymerase
- replication begins at the origin while transcription starts at promoters

What occurs when DNA and RNA polymerases have head-on-collisions?

halt to replication and pre-mature termination of transcription; replication must be restarted for the entire genome to be copied

Where does replication usually begins?

replication usually begins at a single origin

How do bacteria avoid head-on collisions?

essential genes are transcribed in the same direction that replication occurs

How does replication occur in bacteria?

it beings at a single origin, occurs continuously on both strands, and is not segregated in time from transcription (transcription and translation occur simultaneously)

How has replication occur in eukaryotes to prevent head-on- collisions?

it occurs during S phase, allowing transcription to occur without risk of colliding with replication complexes

What is the DNA-protein paradox?

if nucleic acids carry the coding instructions for proteins, how could proteins be generated with out them

What solves the DNA-protein paradox?

RNA can serve as a biological catalyst; catalytic RNAs can catalyze peptide bonds between amino acids

Ribosymes

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

How did studying replication reveal evidence that supported that the original genetic material was RNA?

led to discovery of self-replicating ribosomes, which served as both carriers of genetic info and catalysts that drove chemical reactions

Why is DNA used instead of RNA?

DNA is more stable and leads to more faithful replication

How does the difference chemical structure compare between RNA and DNA affect their relative stabilities?

both are ribose sugars, but RNA has a free, hydroxyl group that degrades rapidly under alkaline conditions; DNA lacks this hydroxyl group so it is a more stable molecule

Why do RNA molecules form secondary structures?

due to hydrogen bonding between complementary and secondary bases on the same strand

How does RNA or DNA differ?

RNA usually consists a single polynucleotide strand, whereas DNA normally consists of two polynucleotide strands joined by hydrogen bonding between complementary bases

hairpins

short complementary regions within a nucleotide strand can pair and form secondary structures

Why is it important that RNA molecules are able to form secondary structures?

it provides RNA far more variation in function than DNA molecules

Ribsomal RNA (rRNA)

ribosomal protein subunits that make up the ribosome

messenger RNA (mRNA)

carries the coding instructions for a polypeptide chain from DNA to the ribosome; specifies the sequence of amino acids in a polypeptide chain and provides a template for the joining of those amino aids

pre-messenger RNAs

immediate products of transcription in eukaryotic cells; modified extensively before becoming mRNA and exiting the nucleus for translation into protein

transfer RNA (tRNA)

serves as the link between coding sequence of nucleotides in a mRNA molecule and the amino acid sequence of a polypeptide chain; attaches to one particular type of amino acid and helps incorporate that amino acid into a polypeptide chain

small nuclear RNAs (snRNAs)

combines with small protein subunits to form small nuclear ribonucleoproteins (snRNPs); participate in the processing of RNA; converted pre-mRNA to mRNA

RNA interference

a process in which small RNA molecules help trigger the degradation of mRNA or inhibit its translation into protein

What are the 2 main types of RNA that are involved in RNA interference?

1.) microRNAs (miRNAs)
2.) small interfering RNAs (siRNAs)

What are the main types of RNA?

1.) Ribosomal RNA (rRNA)
2.) messenger RNA (mRNA)
3.) transfer RNA (tRNA)
4.) Pre-messenger RNA (pre-mRNA)
5.) Small nuclear RNA (snRNA)
6.) MicroRNA (miRNA)
7.) Small interfering RNA (siRNA)

How are cellular RNAs synthesized?

from DNA templates through the process of transcription

How is transcription different from replication?

in replication, all of the nucleotides in the DNA molecule are copied, but in transcription, only parts of the DNA molecule are transcribed into RNA

Why are only parts of the DNA molecule transcribed into RNA?

because not all gene products are needed at the same time or in the same cell; it would be inefficient to constantly transcribe all of the cell's gene

What does it mean that transcription is a highly selective process?

individual genes are transcribed only as their products are needed

True or false: All RNA is copied from DNA.

False. Some viruses copy RNA molecules directly from RNA.

What RNAs are transcribed in both prokaryotic and eukaryotic cells?

- messenger RNA (mRNA)
-Ribosomal RNA (rRNA)
- transfer RNA (tRNA)

What are the 3 major components that are required for transcription?

(the small for replication)
1.) A DNA template
2.) Raw Materials (ribonucleotide triphosphate)
3.) Transcription apparatus (proteins)

How did scientist describe RNA synthesis appearing on a microscope?

Christmas tree-like structures: "tree trunks" were DNA molecules, branches were RNA

How did scientist reveal the difference between DNA and RNA on a microscope?

when deoxyribonuclease was added, the central fibers (trunks) disappeared, whereas when ribonuclease was added, the strings (branches) disappeared

What happens as the transcription apparatus moves down the DNA?

more of the template is transcribed so RNA molecules lengthen

template strand

the nucleotide strand used for transcription

non-template strand

the other strand, that is not transcribed

What is the relationship between RNA and its template strand.

RNA is complementary and antiparallel to its template strand

What is the direction of transcription?

new nucleotides are added to the 3 -OH group of the growing RNA; transcription occurs in the 3' to 5' direction

What is the relationship between the RNA molecule and the non-template strand?

they have the same polarity and base sequence, except the RNA strand contains a U instead of a t

True or false: Each gene is transcribed from a single DNA strand.

False. Different genes may be transcribed from different strands.

transcription unit

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

What are the 3 main parts of the transcription unit?

1.) a promoter
2.) an RNA-coding region
3.) a terminator

promoter

a DNA sequence that the transcription apparatus recognizes and binds

What is the function of the promoter?

to indicate which of the two strands is to be read as the template and the direction of transcription; determines the transcription start site

What is the relationship between the promoter and the transcription start site?

the promoter is located next to the transcription start site but is not transcribed

RNA-coding region

a sequence of DNA nucleotides copied into an RNA molecule

terminator

a sequence of nucleotides that signals where transcription is to end

When does transcription stop?

after the terminator has been copied into the RNA

upstream

before the transcription site

downstream

after the transcription start site

ribonucleoside triphosphate (rNTPs)

ribose sugar and a base (nucleoside) attached to three phosphate groups

How is RNA synthesized from ribonucleoside triphosphates?

2 phosphate groups are cleaved from the incoming ribonucleoside triphosphate; the remaining phosphate group participates in a phosphodiester bond

What direction are the nucleotides added?

nucleotides are always added to the 3' end of the RNA molecule, and the direction of the transcription is 5' to 3'

RNA polymerase

carries out all the required steps

accessory proteins

enhance the action of RNA polymerase

Core enzyme

two copies of alpha; one copy beta, beta prime, and omega; catalyzes the elongation of the RNA molecule by the addition of RNA nucleotides

sigma factor

controls the binding of RNA polymerase to the promoter

holoenzyme

the sigma factor associated with the core enzyme

What is the sigma factor required for?

promoting binding and iniation

What is the function of core enzyme?

it catalyzes the elongation of the RNA molecule by the addition of RNA molecules

RNA polymerase I

transcribes RNA polymerase i

RNA polymerase II

transcribes other small RNA molecules; transcribes pre-mRNAs

RNA polymerase III

transcribes tRNAs and small rRNAs

What are the threes stages of transcription?

1.) Initiation
2.) Elongation
3.) Termination

Initiation

the transcription assembles on the promoter and begins the synthesis of RNA

elongation

DNA is threaded through RNA polymerase and the polymerase unwinds the DNA and adds new nucleotides, one at a time, to the 3' end of the growing RNA strand

termination

the recognition of the end of the transcription unit and the separation of the RNA molecule from the DNA template

What are the steps of initiation?

1.) promoter recognition
2.) formation of the transcription bubble
3.) creation of the first bonds between rNTPs
4.) the escape of the transcription apparatus from the promoter

What is required for transcription initiation?

the transcription apparatus must recognize and bind to the promoter

What does the binding of RNA polymerase to the promoter determine?

which parts of the DNA template are transcribed and how often; the frequency of transcription

What is the relationship between promoters and the RNA-coding region?

promoters are adjacent to the RNA coding region

consensus sequences

short stretches of common nucleotides; the set of the most commonly encountered nucleotides among sequences that possess considerable similarity; implies that the sequence is associated with important information

-10 consensus sequence (pribnow box)

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

What is the nucleotide sequence associated with the pribnow box (-10 consensus sequence)?

TATAAT

Where is the Pribnow box (-10 consensus sequence) located?

10 base pairs upstream of the start site

-35 consensus sequence

consensus sequence 35 nucleotides upstream of the start site

How is the holoenzyme associated with the -10 and -35 consensus sequences?

the sigma factor associates with the core RNA polymerase enzyme to form a holoenzyme, which binds to the -35 and -10 consensus sequences in the DNA promoter

How does the holoenzyme bind to the promoter?

it initially binds weakly to the promoter but then undergoes a change in structure that allows it to bind more tightly and unwind the double stranded DNA

Where does unwinding occur (and why?)

the holoenzyme that is bonded to the -10 consensus sequence starts unwinding there and the extends downstream, including the start site

Where does the sigma factor bind to?

the -35 and -10 consensus sequences

How is the direction of transcription determined?

the locations of the consensus sequences

How does RNA polymerase begin the synthesis of an RNA molecule?

RNA polymerase pairs the base at the start site on the DNA template strand with its complementary base on an rNTP

True or false: A primer is required for transcription.

False. Since RNA has a free OH group, no primer is needed

What happens to RNA polymerase at the end of initiation?

RNA polymerase undergoes a change in its conformation and so is no longer able to bind to the consensus sequences in the promoter

Why is it important that RNA polymerase can undergo a change in confirmation?

it allows the polymerase to escape from the promoter and begin transcribing down stream after it is done initiating RNA transcription at another site

What occurs as RNA polymerase moves downstream?

the RNA polymerase unwinds the DNA at the leading (downstream) edge of the transcription bubble, joining nucleotides of the growing RNA molecule

transcription bubble

a short stretch of about 18 nucleotides of unwound DNA; where transcription takes place and RNA is continuously synthesized

How is DNA affected by the transcription apparatus?

as the transcription apparatus moves down the template, it generates positive supercoiling ahead of the transcription bubble and negative supercoiling behind it (DNA is unwound and rewind)

Why is topoisomerase needed during transcription?

topoisomerase enzymes relieve the stress associated with the unwinding and reminding of DNA in transcription

How do secondary structures influence transcription?

they cause RNA polymerase to pause during the elongation stage of transcription

How is the accuracy of transcription increased?

RNA polymerase is capable of proofreading and can backtrack and cleave nucleotides if a nucleotide is found not to match the template and then replace it and transcribe forwards

What is the relationship between consensus sequences, the promoter, and RNA polymerase?

RNA polymerase binds to the consensus sequences of the promoter

When does RNA polymerase stop transcribing?

nucleotides are added to the 3' end of the growing end of the RNA molecule until it transcribes a terminator and then stops after the terminator is transcribed

True or false: The only thing needed to end transcription is the end of RNA polymerase adding nucleotides?

False. Other events are needed to end transcription.

What is needed to bring an end to transcription?

1.) RNA polymerase stops synthesizing RNA
2.) the RNA molecule must be released from RNA polymerase
3.) the RNA molecule must dissociate fully from the DNA
4.) RNA polymerase must detach from the DNA template

What are the 2 major types of terminators?

1.) Rho-dependent terminators

2.) Rho-independent terminators

Rho-dependent terminators

able to cause the terminator of transcription only in the presence of the rho factor