Chapter 7: From DNA to Protein

RNA polymerase steps

Binds, elongation, transcribes, and releases

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex

Terminator

A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene

In bacteria,

A subunit of RNA polymerase, the sigma factor is responsible for recognizing the promoter sequence on DNA. Does not have to unzip the DNA strand

General transcription factors

Accessory proteins that assemble on the promoter and position the RNA polymerase II and pull apart the DNA double helix allowing polymerase to begin transcription. TFIIB, TFIID

RNA is single stranded

Can fold into a variety of shapes (3D)

A eukaryotic RNA must go through several RNA processing steps before leaving the nucleus

Capping and polyadenylation occur only on RNA transcripts destined to become mRNA molecules (precursor mRNAs)

exons

Coding segments of eukaryotic DNA.

TFIIH

Contains a DNA helicase to unwind DNA and activates RNA polymerase II by phosphorylation

RNA can base pair with

DNA

The RNA transcript is elongated one nucleotide at a time and has nucleotide sequence the same as the

DNA template strand

Prokaryote

DNA-mRNA-protein all in cytoplasm

Eukaryotes

DNA-premRNA-mRNA-protein

Spilceosome

Enzyme, made of snRNPs. recognize sequence, cut and paste exons together

RNA strand is not __ to the DNA template strand

Hydrogen bonded

Eukaryotic cells have three RNA polymerases

I, II, III

__ are small RNAs that serve as key regulators of eukaryotic gene expression

MicroRNAs (miRNAs)

poly-A tail

Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.

RNA Capping

Modifies the 5' end of the RNA transcript (synthesized first), RNA is capped by the addition of an atypical nucleotide , a guanine nucleotide bearing a methyl group. Occurs after RNA polymerase II produces 25 nucleotides of RNA

Introns

Noncoding segments of nucleic acid that lie between coding sequences.

precursor mRNAs

Primary RNA transcripts that are copied from a gene that are processed into mature mRNAs

RNA splicing

Process by which the introns are removed from RNA transcripts and the remaining exons are joined together. RNA is now a functional mRNA molecule that can leave the nucleus and be translated into a protein

Polyadenylation

Provides a newly transcribed mRNA with a special structure at its 3' end, 3' end is trimmed by an enzyme that cuts the RNA chain at a particular sequence of nucleotides, the transcript is finished off by a second enzyme that adds a series of repeated adenine nucleotides to the cut end (Poly A-tail)

One of the DNA strand acts as a template for synthesis of

RNA

When a certain protein is needed by the cell, the nucleotide sequence of the segment of a DNA molecule is copied into

RNA

Exons and introns are in both

RNA and DNA

__ catalyzes the formation of phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain

RNA polymerase

After capping and as RNA polymerase II continues to transcribe the gene,__ begins

RNA splicing

TFIIB

Recognizes BRE element in promoters; accurately positions RNA polymerase at the start site of transcription

Alternative splicing

Regulated process during gene expression that results in a single gene coding for multiple proteins. 95% of genes undergo this method

__ is joined together by RNA polymerase to begin synthesizing the RNA chain

Ribonucleoside triphosphate

__ are added to the growing RNA chain

Ribonucleotide

__ is an RNA molecule that forms the structural and catalytic core of the ribosome and translates mRNA into proteins

Ribosomal RNA (rRNA)

promoter

Specific region of a gene where RNA polymerase can bind and begin transcription. When RNA polymerase is bound to promoter, it opens up the double helix in front of the promoter to expose the nucleotides

Promoters contain a DNA sequence called the

TATA box

TATA box is recognized by a subunit of TFIID called the

TATA-binding protein (TBP)

The binding of TFIID enables the adjacent binding of

TFIIB

__ prines apart the double helix at the transcription starting point using ATP hydrolysis and exposes the template

TFIIH

Chain elongation continues until RNA polymerase encounters the

Terminator or stop site

TFIID

The first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP)

How an RNA polymerase determines which strand of DNA to use as a template:

The orientation of the promoter determines which direction the gene is transcribed and which strand is the template strand. The structure of the promoter has a certain polarity, it contains 2 different nucleotide sequences

Gene expression

The process where info is encoded in a DNA sequence is translated into a product that has some effect on a cell/organism

__ is where RNA polymerase must be able to recognize the start of a gene and bind firmly to DNA at this site.

The transcription start site

__ act as adaptors that 'reads' a codon in mRNA and adds the correct amino acid to the growing polypeptide chain

Transfer RNA (tRNA)

RNA polymerase

Unwinds the DNA helix, uses ribonucleoside for phosphates as substrates so it catalyzes the linkage of ribonucleotides, can start an RNA chain without a primer, makes one mistake every 10^4 nucleotide copied to RNA, & can proofread but not as efficient

RNA polymerase II transcribes

eukaryotic genes (that encodes proteins and miRNAs) and noncoding RNAs

When the polymerase finished transcribing a gene, it is released from the DNA the

phosphates on its tail are stripped off by protein phosphatase and ready to find a new promoter

mRNA molecules bind to proteins such as __ to be transported to the cytosol

poly-A binding proteins, cap-binding complex, and protein that bind to spliced mRNAs

RNA is a linear polymer made of 4 different nucleotide sequences linked together by

polydiester bonds

Site of phosphorylation is a long tail that extends from the

polymerase

RNA polymerase latches on tightly if it encounters the gene called

promoter

RNA copies are used to direct synthesis of the

protein

Genes carried in a cells DNA specify the amino acid sequences of

proteins

Transcriptions begins with

the opening and unzipping of a small portion of DNA double helix to expose the bases on each strand

DNA-RNA

transcription

RNA molecule can be

translated over again

When RNA polymerase collides with a DNA molecule, the enzyme sticks

weakly to the double helix

RNA has

structural, regulatory or catalytic roles

RNA polymerase III transcribes

tRNA, 5S rRNA and genes for small RNAs

Factor VIII gene encode the protein Factor VIII contains __ exons

26, Mutations in this gene are responsible for hemophilia

B-globin gene encodes hemoglobin contains __ exons

3

The terminator is transcribed into the__ end of the new RNA strand

3'

RNA chain grows in what direction

5' to 3'

lariat

cut out intron

Protein synthesis takes place on ribosomes in the

cytoplasm

The RNA molecules encoded by these genes are called

messenger RNA (mRNA)

RNA polymerase I transcribes

most rRNA genes,

Transcription takes place in the

nucleus

The incoming __ drives the reaction forward

ribonucleoside triphosphates (ATP, CTP, UTP, GTP)

The nucleotides in RNA are

ribonucleotides. A,G,C,U

In bacteria, a group of genes is transcribed as a

single mRNA

In eukaryotes, mRNA carries info transcribed from one gene, which codes for a

single protein

RNA splicing is carried out by

small nuclear RNAs (snRNPs)

snRNP

small nuclear ribonucleoproteins; recognize the splice sites in the pre-mRNA; located in the nucleus and are composed of proteins and RNA. contain U1, U2. U4, U5, U6

mRNA must be transported out of the nucleus through

small pores in the nuclear envelope