BIO 329 THE CENTRAL DOGMA DNA TO RNA

genetic information directs the synthesis

of proteins

DNA is the genetic material within

the nucleus

replication creates new copies of

DNA

transcription creates an RNA using 

DNA information

translation creates a protein using

RNA information

The RNA intermediate allows organism to 

amplify the gene expression and regulate gene expression

RNA chemical structure contains what ribose

sugar

deoxyribose is a sugar used in 

DNA by the presence of an additional -OH group 

RNA contains the base uracil, which differs from thymine, by the absence of a 

-CH3 group 

The chemical linkage between nucleotides in RNA—a phosphodiester bond—is the same as that in

DNA

RNA molecules can fold into specific structures that are held together by what bond?

hydrogen bonds between different bases

RNA is largely single-stranded, but it often contains

short stretches of nucleotides that can base-pair with complementary sequences found elsewhere on the same molecule

base pair interactions allow an RNA molecule to fold into a

3D structure that is determined by its sequence of nucleotide

Transcription of a gene produces an

RNA complementary to one strand of DNA

the bottom strand of DNA is called the

template strand because it is used to guide the synthesis of the RNA molecule

the non template strand is sometimes called the

coding strand because its sequence is equivalent to the RNA product

An RNA molecule is usually depicted by

the 5’ end and moving to the left

type of RNA produced in cells

messenger RNA, ribsosomal RNA, MicroRNAs, Transfer RNA, Small interfering RNA’s, long non coding RNAs

what does messenger RNA do

Code for proteins

what does Ribosomal RNA do?

form the core of the ribosome’s structure and catalyze protein synthesis

what does mircoRNA do?

regulate gene expression

what does Transfer RNAs do?

serve as adaptors between mRNA and amino acids during protein synthesis

what does small interfering RNA do?

provide protection from viruses and proliferating transposable elements 

what does long noncoding RNAs do?

acts as scaffolds and serve other diverse functions

what does other noncoding RNA do?

Used in RNA splicing, gene regulation, telomere maintenance, and other processes

The complimentary messenger RNA strand that would be synthesized from the DNA base sequence of CTGAC would be...?

GACUG

What are the 3 polymerases in eukaryotic cells

DNA polymerase 1, DNA polymerase 2, DNA polymerse 3

what genes do DNA polymerase 1 transcribe

Most rRNA genes

what genes do DNA polymerase 2 transcribe

all protein coding genes, miRNA genes, plus genes for other noncoding RNA

what genes do DNA polymerase 3 transcribe

tRNA genes, 5S rRNA gene, genes for many other small RNAs

A transcription unit is defined as

that region of DNA that includes the signals for transcription initiation, elongation, and termination

DNA-dependent RNA polymerase is the enzyme responsible for the

polymerization of ribonucleotides into a sequence complementary to the template strand of the gene

The enzyme; polymerase attaches at a specific site

the promoter on the template strand

enzyme attaching to the promoter site is then followed by

initiation of RNA synthesis at the starting point, and the process continues until a termination sequence is reached.

Signals in the DNA Tell RNA Polymerase

where to start and stop transcription

promoter in transcription sites where RNA polymerase

binds and start transcription

terminator is the

site where transcription ends

sigma factor in bacteria recruits

RNA polymerase

bacterial RNA polymerase contains a subunit called 

sigma factor

sigma factor recognizes

the promoter of the gene

Once transcription has begun, sigma factor is

released, and the polymerase moves forward and continues synthesizing the RNA

. Elongation continues until the polymerase encounters a sequence in the gene called the

terminator

After transcribing this sequence into RNA, the enzyme

halts and releases both the DNA template and the newly made RNA transcript

The polymerase then reassociates with a free sigma factor and searches for another promoter to

begin the process again

All bacterial promoters contain DNA sequences at positions

-10 and -35

. The numbers above the DNA indicate the positions of nucleotides counting from the first nucleotide transcribed, which is designated

+1

transcription begins at the _ , proceeds through the _ and ends at the _

promoter, coding regions, and terminator

In eukaryotes, the core promoter of a transcription unit generally includes:

TATA box, initiator

On an individual chromosome, some genes are transcribed using

one DNA strand as a template and others are transcribed from the other DNA strand

RNA polymerase always moves in the

3’-5’ direction with respect to the template DNA strand

the strand that will serve as the template is determined by the

polarity of the promoter sequences at the beginning of each gene

To begin transcription, eukaryotic RNA polymerase II requires

a set of general transcription factors.

Most eukaryotic promoters contain a DNA sequence called the

TATA box

The TATA box is recognized by a subunit of the

the general transcription factor TFIID, called the TATA-binding protein (TBP)

The binding of TFIID, which distorts the DNA, enables

the adjacent binding of TFIIB.

the rest of the genreal transcription factors then assemble at the

promoter, using energy provided by ATP hydrolysis

TFIIH opens the

double helix at the transcription start point, exposing the template strand of the gene

TFIIH also phosphorylates RNA polymerase II, releasing its

attachment to the general transcription factors and allowing it to begin transcription

The site of phosphorylation is a long polypeptide “tail” that extends from the

polymerase

Once the polymerase moves away from the promoter, most of the general transcription factors are released

form the DNA; the exception is TFIID

A set of elongation factors assemble on the actively transcribing

RNA polymerase to facilitase access to the DNA

Which transcription factor is responsible for recognizing the TATA box during PIC assembly?

TBP (part of TFIID)

In Eukaryotes, Protein-coding Genes Are Interrupted by

noncoding sequences called introns

A bacterial gene consists of a single stretch of

uninterrupted nucleotide sequence that encodes the amino acid sequence of a protein

the protein-coding sequences of most eukaryotic genes (exons) are interrupted by

noncoding sequences 

pre m-RNA is modified in 3 ways before exiting nucleus in eukaryotes

5’ capping: adding 7- methylguanosine 

polyadenylation: adding AAAAAAAAA

splicing: intron removal

processing of messenger RNA 5’ cap

1. a methylguanosine “cap: is added to the 5’ end of the transcript (5’-5’ triphosphate bridge)

2. significance: prevent digestion, aids in export from nucleus, aids in initiation of translation

eukaryotic mRNA molecules are modified by

capping and polyadenylation

A eukaryotic mRNA has a cap at the

5’ end

A eukaryotic mRNA has a tail at the

3’ end

The noncoding portion at the 5′ end is called the

5′ untranslated region, or 5′ UTR, and that at the 3′ end is called the 3′ UTR.

Which of the following proteins is deposited near exon–exon junctions after splicing and is important for nonsense-mediated decay (NMD)?

Exon Junction Complex (EJC)

if you wanted to extract all mRNAs from the total pool of RNA, which characteristic of mRNA can be used?

mRNA poly-A-tail

introns

non coding regions, need to be removed before mRNA exist the nucleus

Exons

coding regions

The special sequences are recognized primarily by

small nuclear ribonucleoproteins (snRNPs), which direct the cleavage of the RNA at the intron–exon borders and catalyze the covalent linkage of the exon sequences.

Special nucleotide sequences in a pre-mRNA transcript signal the

beginning and the end of an intron

Splicing is carried out by a collection of RNA–protein complexes called

snRNPs

In the first steps of splicing, U1 recognizes the

5’ splice site

U2 recognizes the

lariat branch-point site through complementary base-pairing

U6 snRNPs will

then “double-checks” the 5′ splice site by displacing U1 and base-pairing with the same intron sequence itself. This “rereading” step improves the accuracy of splicing by confirming the 5′ splice site before carrying out the splicing reaction

conformational changes in U2 and U6—triggered by the

hydrolysis of ATP by spliceosomal proteins

Once the splicing reactions have occurred

the spliceosome deposits a group of RNA-binding proteins, known as the exon junction complex, on the mRNA to mark the splice site as successfully completed

During the catalytic activation of the spliceosome, which rearrangement is essential?

U1 is displaced from the 5′ splice site by U6

RNAi is a natural biological process that regulates gene expression by

“interfering” with messenger RNA (mRNA), which carries DNA's instructions for making new proteins.

Medicines use RNA interference (RNAi) to

“silence” or turn off the production of specific genes that cause disease or that contribute to disease such as cardiovascular diseases, viral infections, and cancer.