FUNDABIOCHEM MIDTERMS TOPIC 2

Transcription

is a process in which ribosomal nucleic acid (RNA) is synthesized from DNA.

ribosomal nucleic acid (RNA); DNA

Transcription is a process in which —— is synthesized from ——.

Gene

refers to the functional unit of the DNA that can be transcribed.

DNA

Gene refers to the functional unit of the —— that can be transcribed.

DNA; RNAs

The entire molecule of — is not expressed in transcription. — are synthesized only for some selected regions of DNA.

primary transcript

The product formed in transcription is referred to as —

nucleoid ; cytoplasm

DNA is located in the — region of the —

True

Transcription and translation happen simultaneously. True or false?

exon (coding) and intron (non-coding) regions; DNA → transcription → pre-mRNA → processing → splicing → mRNA → nuclear export → cytosol → translation → protein.

In a eukaryotic diagram of transcription, DNA is located in the nucleus and features these two regions. Moreover, what is the general flow or process of this?

TEMPLATE STRAND (Antisense strand)

The DNA strand actually used as the template for RNA synthesis.

RNA synthesis

Template strand (antisense strand) is the DNA strand actually used as the template for —

RNA polymerase

What reads the template (antisense) strand?

3' → 5' direction

What direction does the template (antisense) strand read in?

complementary

Template (antisense) strand is — to the RNA produced.

CODING STRAND (Sense strand)

is the DNA strand not directly used as the template.

RNA

CODING STRAND (Sense strand) has the same base sequence as —

T (thymine) ; U (uracil)

CODING STRAND (Sense strand) has the same base sequence as the RNA, except DNA has — and RNA has —

amino acid ; protein

CODING STRAND (Sense strand)’s sequence corresponds to the — sequence of the —

Initiation, Elongation, and Termination

Transcription is divided into three steps for both prokaryotes and eukaryotes: —, —, —

elongation; initiation ; termination

The process of — is highly conserved between prokaryotes and eukaryotes, but — and — are somewhat different.

Core Enzyme

In prokaryotic transcription, this is composed of five core subunits with a total mass of about 400 kDa.

five ; 400 kDa

In prokaryotic transcription, core enzyme is composed of — core subunits with a total mass of about —.

Two Alpha (α) subunits

In prokaryotic transcription, these build the structure and assemble the enzyme.

Beta (β) subunit

In prokaryotic transcription, this contains the main catalytic activity to build RNA.

Beta-prime (β′) subunit

In prokaryotic transcription, this binds nonspecifically to DNA.

Omega (ω) subunit

In prokaryotic transcription, this helps assemble the holoenzyme and keeps it stable.

Sigma (σ) Factor

In prokaryotic transcription, this binds to the core enzyme to create the complete holoenzyme.

Sigma (σ) Factor

In prokaryotic transcription, it guides the enzyme to specific promoter sequences on the DNA.

mRNA

carries information for protein synthesis.

rRNA

part of ribosomes

tRNA

carries amino acids during translation.

small regulatory RNAs

what other types of RNA can prokaryotic transcription produce?

PROMOTER REGION

In prokaryotic transcription, it is a specific sequence of DNA located near the beginning of a gene.

DNA ; beginning of a gene

The promoter region in a prokaryotic transcription is the specific sequence of — located near the —

recognition site ; binding site ; transcription machinery

In prokaryotic transcription, the promoter region acts as a — and — for the — and determines where transcription begins.

promoter region

determines where transcription begins in prokaryotic transcription

1. Pribnow box (TATA box)

2. The '-35' sequence

In prokaryotic transcription, there are two base sequences on the coding DNA strand which the sigma factor of RNA polymerase can recognize for initiation:

sigma factor ; RNA polymerase ; initiation

In prokaryotic transcription, there are two base sequences on the coding DNA strand which the — of — can recognize for — : Pribnow box (TATA box) and The '-35' sequence

-35 region

Recognition site in the promoter region of DNA. Contains a base sequence TTGACA, located about 35 bases (upstream) away on the left side from the site of transcription start.

DNA ; TTGACA ; 35 bases ; transcription start

-35 region: Recognition site in the promoter region of —. Contains a base sequence —, located about — (upstream) away on the left side from the — site.

-10 region (Pribnow box / TATA box)

Consists of 6 nucleotide bases (TATAAT), located on the left side about 10 bases away (upstream) from the starting point of transcription.

6 (TATAAT) ; 10 bases

-10 region (Pribnow box / TATA box): Consists of — nucleotide bases, located on the left side about — away (upstream) from the starting point of transcription.

+1 region

Nucleotides that start transcription.

TTGACA region (-35 sequence) ;

TATAAT region (-10 sequence) ;

DNA duplex ;

17 bp

In prokaryote initiation, RNA-polymerase recognizes the —, and slides to the —, then opens the —. The unwound region is about —.

RNA-polymerase ; unwound region

In prokaryote initiation, — recognizes the TTGACA region (-35 sequence), and slides to the TATAAT region (-10 sequence), then opens the DNA duplex. The — is about 17 bp.

+1 site

triphosphate

5'-pppG

3'-OH

RNA polymerase

transcription initiation complex

In initiation steps:

1. RNA polymerase positions itself at the —

2. The first nucleotide enters as a —.

3. RNA initially has a — structure.

4. Additional nucleotides are then added to the —.

5. The assembled promoter, —, and initiating nucleotides constitute the —.

RNA polymerase

first nucleotide

RNA

Additional nucleotides

assembled promoter

nucleotides

In initiation steps:

1. — positions itself at the +1 site.

2. The — enters as a triphosphate.

3. — initially has a 5'-pppG structure.

4. — are then added to the 3'-OH.

5. The —, RNA polymerase, and initiating — constitute the transcription initiation complex.

what is the transcription initiation complex formula

3',5' phosphodiester bond

Sigma (σ) subunit falls off from the RNA-pol once the first — is formed.

Sigma (σ) subunit

— falls off from the RNA-pol once the first 3',5' phosphodiester bond is formed.

DNA template ; elongation

The core enzyme moves along the — to enter the — phase.

Elongation ; σ

— phase begins with releasing the — subunit from the RNA polymerase.

σ subunit

DNA template

mRNA

5' to 3'

40 nucleotides per second

The dissociation of the — allows the core enzyme to proceed along the —, synthesizing — in the — direction at approximately — rate.

3' → 5'

5' → 3'

RNA polymerase reads DNA —, but synthesizes RNA —.

termination

Transcription ends when — signals are reached.

RNA transcript ; RNA polymerase

In termination in prokaryotes, — is released. — dissociates from the DNA.

Rho-Dependent Termination ; ATPase ; RNA

— is where a specific protein, named Rho factor (ρ), acts as — and terminates transcription and releases —.

Rho factor (ρ)

is responsible for the dissociation of RNA polymerase from DNA.

rut site (Rho utilization site) ; C-rich

In the binding of Rho-Dependent Termination, Rho binds to the —, a — region.

5' → 3' direction ; RNA polymerase ; ATP hydrolysis

In the translocation of Rho-Dependent Termination, Rho moves along the RNA in the — direction, following —, using energy from —.

RNA polymerase;

termination;

Rho;

transcription complex

In the pausing of Rho-Dependent Termination, — pauses at a — - associated site, allowing — to catch up with the —

Rho

RNA-DNA hybrid

RNA

RNA polymerase

DNA

In the dissociation of Rho-Dependent Termination, — disrupts the —, releasing the — transcript and separating — from the — template.

Rho-Independent Termination

hairpins

RNA

palindromes

The termination in this case is brought about by the formation of — of newly synthesized —.

This occurs due to the presence of —.

hairpin loop structure

slows down

In Rho-Independent Termination, complementary sequences base pair to form a —. RNA polymerase —, thus termination happens.

RNA POLYMERASE I

Responsible for the synthesis of precursors for the large ribosomal RNAs (rRNAs).

RNA POLYMERASE II

Synthesizes the precursors for mRNAs and small nuclear RNAs (mRNAs & SnRNAs).

RNA POLYMERASE III

Participates in the formation of tRNAs and small ribosomal RNAs (tRNAs & small rRNAs).

large ribosomal RNAs (rRNAs)

RNA POLYMERASE I: Responsible for the synthesis of precursors for the —.

mRNAs

small nuclear RNAs (mRNAs & SnRNAs).

RNA POLYMERASE II: Synthesizes the precursors for — and —

tRNAs ; small ribosomal RNAs (tRNAs & small rRNAs).

RNA POLYMERASE III: Participates in the formation of — and —

Hogness box (or TATA box)

promoter region in eukaryotic transcription

Located on the left about 25 nucleotides away (upstream) from the starting site of mRNA synthesis.

25 ; mRNA synthesis

promoter region in eukaryotic transcription

Hogness box (or TATA box): Located on the left about — nucleotides away (upstream) from the starting site of —.

CAAT box

promoter region in eukaryotic transcription

Another site of recognition between 70 and 80 nucleotides upstream from the start of transcription.

70 and 80

promoter region in eukaryotic transcription

CAAT box: Another site of recognition between — and — nucleotides upstream from the start of transcription.

RNA-polymerase II

six

(TFII A - TFII H)

TFs

enzyme RNA polymerase

Initiation in Eukaryotes

1. — does not bind the promoter directly.

2. RNA-pol II associates with — transcription factors, —.

3. A large number of transcription factors interact with eukaryotic promoter regions.

4. In humans, about six transcription factors have been identified (TFIID, TFIIA, TFIIB, TFIIF, TFIIE, TFIIH).

5. It is postulated that the — bind to each other, and in turn to the — .

True

The elongation in eukaryotes is similar to that of prokaryotes. True or false?

nuclear membrane

In eukaryotic elongation, the transcription and translation do not take place simultaneously since they are separated by the —.

RNA-polymerase II

3' → 5'

5' → 3'

PRE-mRNA

ELONGATION IN EUKARYOTES

Reads DNA —;

Synthesizes RNA —

Creates a —.

pre-mRNA;

polyadenylation signal: 5'—AAUAAA—3’

3'-end processing

In termination involving eukaryotes, when RNA polymerase transcribes the gene, it produces the — . It reaches the —. This is the important signal for —

nascent RNA

primary transcript

In post-transcriptional modifications, the —, also known as — needs to be modified to become functional tRNAs, rRNAs, and mRNAs. The modification is critical to eukaryotic systems.

capping ; 5’

tailing ; 3’

mRNA splicing

Post-transcriptional modifications include:

— at the — end

— at the — end

—

mRNA

7-methylguanosine

5'-5' triphosphate linkage

In post-transcriptional modifications, specifically involving capping at the 5’ - end, the 5' end of — is capped with — by an unusual —.

RNA TRIPHOSPHATASE

guanylyltransferase

GMP (guanosine monophosphate)

In post-transcriptional modifications, specifically involving capping at the 5’ - end:

An enzyme called — cleaves off one of the three phosphates on the 5' end.

Another enzyme called — adds a — to the 5' end.

methyltransferase

7-methylguanosine (m7G).

S-Adenosyl methionine (SAM)

In post-transcriptional modifications, specifically involving capping at the 5’ - end:

• Then the added guanine is methylated by an enzyme called — to form: —

• Methyl Donor: —.

AAUAA

Poly A- Polymerase; adenine (A); cleaved

In post-transcriptional modifications, specifically involving TAILING AT THE 3' - END,

• Nucleotide Signals at the 3' end are: —.

• — adds many — nucleotides to the 3' end of the — RNA.

• To Initiate Translation Process

• Prevents Degradation by Enzymes

• Stability

• Transportation

PURPOSE/FUNCTIONS OF CAPPING

Exons

matured mRNA

— are the coding sequences that appear on split genes and primary transcripts, and will be expressed to —. (Codes for Amino Acids)

Introns

are the non-coding sequences that are transcripted into primary mRNAs, and will be cleaved out in the later splicing process. (Do not code for Amino Acids).

Small nuclear ribonucleoproteins (snRNPs, pronounced "snurps") ;

spliceosome

Introns and their removal/SPLICING DETAILS

• — bind to pre-messenger RNA (pre-mRNA)/ heteronuclear RNA (hnRNA) in the cell nucleus to help cut out unneeded sections called introns.

• The term — is used to represent the snRNP association with hnRNA at the exon-intron junction.

pre-messenger RNA (pre-mRNA)/ heteronuclear RNA (hnRNA) ; nucleus ; introns

snRNP ; hnRNA ; exon-intron junction

Introns and their removal/SPLICING DETAILS

• Small nuclear ribonucleoproteins (snRNPs, pronounced "snurps") bind to — in the cell — to help cut out unneeded sections called —.

• The term spliceosome is used to represent the — association with — at the —.

Actinomycin D (Dactinomycin)

inhibitors of transcription

• —: Synthesized by Streptomyces. Binds with DNA template strand and blocks the movement of RNA polymerase. Very first antibiotic used for the treatment of tumors.

Rifampin

inhibitors of transcription

• —: Antibiotic widely used for tuberculosis and leprosy. Binds with the β-subunit of prokaryotic RNA polymerase and inhibits its activity.

D-Amanitin

inhibitors of transcription

• —: Toxin produced by mushroom, Amanita phalloides. Tightly binds with RNA polymerase II of eukaryotes and inhibits transcription.

Reverse transcription

• Definition: Biological process of synthesizing a complementary DNA (cDNA) strand from an RNA template (exact reverse of normal cellular transcription).

• Enzyme: Reverse transcriptase.

complementary DNA (cDNA)

Reverse transcriptase

Reverse transcription: Biological process of synthesizing a — strand from an RNA template (exact reverse of normal cellular transcription).

Enzyme: —.

• RNA genomes; host genome

• unstable RNA; stable cDNA

• target RNA

Uses of Reverse Transcription

• Viral Replication: Retroviruses (HIV, HTLV-I) convert — into DNA to integrate into —.

• Gene Expression Analysis & Research: Convert — into — for cloning, sequencing, measurement.

• RT-PCR Diagnostics: Detect and quantify — (viral infections, genetic changes).

proteins;

translation

• The genetic information stored in DNA is passed on to RNA, and ultimately expressed in the language of —.

• The biosynthesis of a protein or a polypeptide in a living cell is referred to as —.

genetic code ; simply codons ; 64

• Three nucleotide (triplet) base sequences in mRNA that act as code words for amino acids constitute the — or —.

• Four bases produce — different combinations (4³) of three base codons.

61

— code for the 20 amino acids found in protein.

UAA, UAG, and UGA

termination codons / non-sense codons

—,—,— are stop signals in protein synthesis. Collectively known as — or —.