Smoczer: Gene expression and regulation

What is central dogma?

DNA -> RNA -> Protein

RNA contains uracil instead of _____ on DNA

thymine

Why is RNA more reactive than DNA?

RNA contains a hydroxyl group on the 2' carbon and DNA has a H

What sugar is in RNA?

Ribose

What makes ribose so unstable?

It's highly susceptible to hydrolysis which makes

RNA, DNA, or both: Nucleotides are joined by phosphodiester bonds

Both

What strand is DNA and RNA?

DNA is usually double and RNA is usually single

What is DNA and RNA secondary structure?

DNAs secondary structure is double helix and RNA has many types of

How stable is DNA and RNA?

DNA is stable and RNA is easily degraded

Ribosomal RNA (rRNA) makes up for what percent of total RNA?

80%

What does rRNA assemble with to form ribosomes?

Proteins

What does transfer RNA (tRNA) do?

Matches genetic information to amino acid sequence during translation

What is the clover leaf structure?

Secondary structure of tRNA that is a key structure in protein synthesis

What does the cloverleaf structure have?

Anticodon loop and acceptor stem of CCA

What is the least abundant RNA?

mRNA

What does mRNA do?

Carries genetic guidelines from DNA for protein synthesis(brings "working copy" of the genome)

mRNA is monocistronic, which means that

carries genetic code for only one protein or polypeptide chain

What's the structure of mRNA?

Has 5' cap, a coding sequence for protein synthesis, and a poly(A) tail

Where are rRNA and tRNA found?

Cytoplasm

Where can you find mRNA?

Nucleus and cytoplasm

What is the function of rRNA?

Structural and functional components of the ribosome

What catalyzes transcription?

RNA polymerases

Do you need a primer for transcription?

No

What direction does transcription go?

5'->3'

Do you proofread in transcription?

No

What do the RNA polymerases do?

Unwind the DNA helix and copy the template strand

Template strand is also known as

antisense(noncoding)

Non-template strand is also known as

sense (coding)

What is a gene promoter?

A sequence of nucleotides in DNA that is recognized by RNA polymerase as the starting point of a gene

Where is the gene promoter located?

Upstream of the transcriptional start site

What is the Base(core) promoter?

The minimum sequence necessary for transcription

What does the TATA-box and initiator do?

Sequences required for binding of general transcription factors

What is the proximal promoter?

Regulatory elements/transcription factor binding sites

What are CAAT and GC boxes?

Regulatory sequences for binding of specific transcription factors

What are distal promoters?

Enhancers/silencers

What are special sequences that increase/decrease transcription rate?

Enhancers/silencers

What is the pre-initiation complex?

6 GTF's + RNA polymerase II(mRNA) assemble near the transcription start site on the promoter

General transcription factors bind to TATA box and recruit the RNA polymerase to the transcription start site to begin ______ at ______ rate.

to begin transcription at basal rate

What is elongation?

RNA polymerase unwinds DNA and adds completmentary ribonucleotide triphosphates to the 3' end of RNA

What is the transcription bubble?

melted DNA helix + RNA polymerase + growing RNA

What is termination?

When RNA polymerase reaches the termination/polyadenylation signal, transcription continues for about 50nt and then the pre-mRNA is released

In the nucleus, post-transcriptional modifications of the pre-mRNA produce the

mature mRNA

After the mature mRNA is produces, it exits through the nuclear pore and enters the cytoplasm for?

translation

Post-transcriptional modifications

7-methyl cap, poly(A) tail, splicing

What is splicing?

Intron removal and exon joining

Where are the splice sites?

intron-expon junctions marked by AG at the 3'-end of exon and GU at 5'-end of intron

What is alternative splicing?

Different regions are removed from the pre-mRNA to form mature mRNAs with various sequences

What are codons?

Triplets in mRNA that specific one of 20 amino acids

What is unambiguous mean?

Each codon only codes for one amino acid

What is degenerate mean?

Some amino acids encoded by more than one codon

What are genetic code properties?

Unambiguous, degenerate, nonoverlapping, comma less, nearly universal

In ribosomes, there are multi-step assembly lines for what?

Protein synthesis

How many sites are there for translation in ribosomes?

3 sites(APE)

Amino acids attach to tRNA catalyzed by what?

Aminoacyl-tRNA synthase

The anticodon on the charged tRNA binds to the codon on the mRNA by what bonding?

Hydrogen bonding

What is the wobble hypothesis?

tRNA can recognize and bind to a sequence that is not perfectly complementary because of the degeneracy of the code

What does AUG pair with on tRNA?

Methionine

Met-tRNA is directed to the P site, while the A and E sites are?

unoccupied

The large ribosomal subunit completes what complex?

Initiation complex

What subunit binds to initiation factor to form the pre initiation complex?

the small ribosomal rubunit

When does termination start?

when the A site reaches STOP codon

What factors recognize the STOP codon and binds to A site causing newly formed polypeptide chains to be released?

Release factors

What are polysomes(polyribosomes)?

Multiple ribosomes attached to a single mRNA allow for synthesis of multiple protein copies to increase the rate of synthesis

What are the 3 post-translational modifications?

Phosphorylation, glycosylation, and hydroxylation

What is protein degradation?

Ubiquitin group marks for destruction and rapidly degraded by proteases

What are transposons?

Mobile fragments of DNA that can move randomly between different sites on chromosomes(genomic variation)

What regulates transcription?

Transcription factors

Enhancers or silencers activate or repress what?

Transcription

What is alternative polyadenylation?

Proteins with alternative polyadenylation sites generate different coding sequences

mRNA is processed to include a termination sequence before the _____

last codon

What is RNA interference?

A small interfering RNA that induces gene silencing by binding to 3'-UTR of the mRNA and prevent its translation or induce degradation