Term
| Points of regulation in the flow of genetic material |
|
Definition
1) Epigenetic inheritance
2) Transcription (creation of mRNA transcript)
3) RNA processing (resulting in mature RNA)
4) Transport to cytoplasm
5) miRNA
6) Translation |
|
|
Term
| What is miRNA? What does it do? |
|
Definition
Micro RNA
- Regulate translation and transcription |
|
|
Term
| What is the principle of genome equivalence? |
|
Definition
| Cells can change phenotypes without changing genotypes |
|
|
Term
| Principles of differential gene expression |
|
Definition
1) Every genome in an organism is identical
2) Genes that are not expressed are not discarded by cell.
3) Only a small percentage of the genome is expressed by a cell. |
|
|
Term
| Exceptions to central dogma of molecular biology |
|
Definition
1) Some RNAs function as RNAs (RNAs can be enzymes)
2) microRNA regulates transcription and translation
3) RNAs and proteins are regulated after synthesis (stability and degradation) |
|
|
Term
| A cell can regulate level of gene expression. What does this mean? |
|
Definition
Genes can produce more or less mRNA transcripts (as many as they want) and translate more or less proteins.
AMPLIFICATION |
|
|
Term
| What is RNA polymerase, how does it work? |
|
Definition
Synthesizes RNA copy of DNA template in 5' to 3' direction.
Doesn't need primer (DNA polymerase requires RNA primer)
- Transcription started and stopped by regulatory sequences in DNA(start signal = promoter, stop signal = terminator) |
|
|
Term
| Steps of prokaryotic transcription |
|
Definition
1) Initiation
- RNA polymerase and sigma factor binds @ promoter -> transcription begins
2) Elongation
- Loss of sigma factor
3) Termination
READ MORE ON THIS IN BOOK |
|
|
Term
|
Definition
Genetic switches are turned off by repression. Repression caused by tryptophan repressors.
Tryptophan (when high levels are present) binds to repressor, takes it from inactive to active. Active repressor = genes are off.
Low tryptophan = gene expression |
|
|
Term
| How are genetic switches turned off or on? |
|
Definition
Off: Repression (tryptophan repressor)
On: Activation (CAP activator protein) |
|
|
Term
| What is CAP activator protein? |
|
Definition
CAP activator protein bound to DNA at binding site.
cAMP binds to activator protein, activates RNA polymerase.
CLARIFY THIS |
|
|
Term
|
Definition
Balances repressors and activators, transcriptional regulation.
High glucose + high lactose = CAP activator not bound (operon off)
Low lactose = Lac repressor bound (operon off)
Low glucose = CAP activator protein bound (operon on IF repressor not bound as well)
Low glucose + low lactose = repressor and CAP activator protein bound. Repressor blocks activator (operon off)
Low glucose + high lactose = CAP activator protein bound (repressor not bound) (OPERON ON) |
|
|
Term
|
Definition
mRNAs = code for proteins
rRNAs = form core of ribosome and catalyze protein synthesis
miRNAs = regulate gene expression
tRNAs = serve as adaptors between mRNA and amino acids during protein synthesis
Others = used in RNA splicing, telomere maintenance, many other processes |
|
|
Term
| Different types of RNA polymerases |
|
Definition
In eukaryotic cells, different RNAs are transcribed by distinct RNA polymerases
RNA polymerase I: ribosomal RNA (nucleolus)
RNA polymerase II: mRNAs, miRNAs (nucleoplasm)
RNA polymerase III: tRNAs, snRNAs (nucleoplasm) |
|
|
Term
| Different combinations of transcription factors results in cell diversity |
|
Definition
|
|
Term
| Explain what Eyeless gene does. |
|
Definition
Eyeless gene (Ey) is necessary and sufficient for eye development.
When Ey gene is artificially expressed in leg precursor cells, eye structure formed on leg.
Pac-6 = Human eyeless gene |
|
|
Term
| Transcription and translation in prokaryotes vs eukaryotes |
|
Definition
Prokaryotes: Coupled transcription and translation (absence of nucleus and nuclear membrane)
- Transcription: Sigma factor on RNA polymerase recognizes promoter region. Sigma factor released after 10 nucleotides. Transcription goes until terminator reached.
- Translation: occurs concurrently, doesn't need to identify 5' end
Eukaryotes: Transcription in nucleus, translation in cytoplasm (ribosomes in cytoplasm)
- 3 RNA polymerases (RNA polymerase II = protein-coding, I & III = tRNA, rRNA)
- Transcriptions factors needed (TATA box, TAF and TFIID factors)
- Translation: tRNA binds to small ribosomal subunit, finds 5' cap on mRNA, searches for start codon to begin translation. |
|
|
Term
| Describe transcription coupled mRNA processing in the nucleus |
|
Definition
Capping factors, Splicing factors, Polyadenylation factors
- Capping factor on 5' end (beginning of mRNA transcription). Without cap on mRNA, RNA processing doesn't occur.
- Polyadenylation on 3' end |
|
|
Term
| How are exon/introns joined and removed? |
|
Definition
Exon/intron junctions and excisions are guided by 3 specific RNA sequences (cis-acting, on same RNA molecule)
Specific RNA sequences indicate intron/exon borders for SPLYSOSOME. OH-part of 3' end of intron attaches to end of 5' exon, OH-part of 5' end of exon attacks original 3' end of intron -> lariat formed.
Exon mRNA sequence results. |
|
|
Term
| Mapping cis-control elements |
|
Definition
Proximal promoters, distal enhancers.
- Eukaryotic regulation areas are very large.
- Without enhancer and promoter, RNA polymerase doesn't work. |
|
|
Term
| Know activators (transcriptional activators), general factors, co-activators (TAFs), Remodelers |
|
Definition
Transcription factors are proteins that bind to DNA at specific sequences using DNA binding domain. They bring RNA polymerase to start transcription. Ex: Heat Shock Factors (HSF), TFIID.
- Often transcribed in response to environmental conditions (like heat for HSF) and increases transcription for targeted genes
Co-activators: Discovery of TAFs showed that multiple transcriptions or other proteins needed to bind in order for RNA polymerase II to transcribe. "Co-activators" sometimes necessary in addition to transcription factors to start transcription. |
|
|
Term
| What is alternative splicing? |
|
Definition
Not all proteins are spliced the same way.
Alternative splicing -> different functions, more diversity |
|
|
Term
|
Definition
Exons are smaller than introns.
- Humans have large introns (compared to fly and worm) -> most of human genome incodes introns.
Introns ARE NOT junk DNA |
|
|
Term
| How is mature RNA transported? |
|
Definition
Mature RNA is bound and stabilized by multiple protein factors.
EJC = exon junction complex
Protein co-factors carry mRNA out of nucleus through nuclear pore complex. |
|
|
Term
|
Definition
| Triplet codons specify amino acids Each RNA strand has 3 possible reading frames (due to triplet nature of codons) |
|
|
Term
| How are amino acids created? |
|
Definition
tRNA binds anticodon to mRNA.
Aminoacyl-tRNA synthetase charges tRNA with appropriate amino acid (specifies amino acid to link to tRNA).
3rd position of mRNA = wobble position. Some codons that vary at wobble position can utilize same tRNA (flexible base pairing) |
|
|
Term
| Start and stop sequences in translation |
|
Definition
Start = AUG (Methionine)
Stop = UAA, UAG, UGA
Sequences in mRNA signal start and stop translation to tRNA. After stop sequence, untranslated region. |
|
|
Term
|
Definition
Ribosomes are protein/RNA machines that translate mRNA into protein.
- Ribosome subunit assembly occurs in nucleolus. (Large and small subunits)
- Protein translation occurs in cytoplasm |
|
|
Term
|
Definition
Ribosomes add amino acids in stepwise fashion. PEPTIDYL TRANSFERASE catalyzes peptide bond formation.
3 functional domains of ribosome (APE, A at 3' end of mRNA)
1) A = aminoacyl-tRNA (charged tRNA) acceptor site
2) P = peptidyl-tRNA (peptide bond forming site)
3) E = exit site for spent tRNA
Small subunit of ribosome = mRNA binding site
Process:
1) tRNA (with amino acid) newly bound to mRNA at A site.
2) P site forms peptide bond between amino acid chain and amino acid on newly bound tRNA.
3) Large subunit translocates (slides to right)
4) Small subunit translocates (slides to right to match large subunit)
5) Old tRNA ejected, amino acid chain builds, cycle continues |
|
|
Term
|
Definition
1) Initiation
- Small ribosomal subunit binds to mRNA with translation initiator factors
- Initiator tRNA moves along RNA searching for start codon.
- Initiation factors dissociate, large ribosomal subunit binds.
- Aminoacyl-tRNA binds to A-site, first peptide bond forms.
2) Elongation
- tRNA (with amino acid) newly bound to mRNA at A site.
- P site forms peptide bond between amino acid chain and amino acid on newly bound tRNA.
- Large subunit translocates (slides to right)
- Small subunit translocates (slides to right to match large subunit)
- Old tRNA ejected, amino acid chain builds, cycle continues
3) Termination
- Stop codon found
- Release factor binds to A-site, amino acid chain ejected
- Large subunit translocates, release factor binds to P-site.
- Ribosome breaks up, detaches from mRNA. |
|
|
Term
| Describe post-transcriptional gene silencing (PTGS) and RNA interference (RNAi) |
|
Definition
RNA interference: MicroRNA (miRNA) or Silencing RNA (siRNA) induces degradation of complementary mRNA.
RNA silencing: READ MORE
miRNA = repress translation
siRNA = degrade mRNA |
|
|
Term
|
Definition
lin-4 is a non-coding microRNA that represses lin-14 translation.
- First to be discovered of miRNAs |
|
|
Term
|
Definition
miR-172 is a miRNA targeting mRNA coding for ap2 transcription.
Overexpression of miR-172 phenocopies ap2 loss of function mutant. |
|
|
Term
| How is protein function regulated after translation? |
|
Definition
1) Phosphorylation
2) Methylation
3) Acetylation
4) Ubiquitination ("Kiss of death", marks proteins for destruction)
5) Sumoylation (similar to Ubiquitination, but doesn't mark proteins for degradation. Modifies function) |
|
|
Term
| What are 3 ways to transmit patterns of gene expression to daughter cells? |
|
Definition
1) Positive feedback loop = transcription regulator activates transcription of its own gene.
2) Propagation of condensed chromatin structure from parent to daughter cell
3) DNA methylation
- Epigenetic inheritance |
|
|
Term
| What is a DNA-binding domain? What does it do? |
|
Definition
DNA binding domain (homeodomain, zinc finger, leucine zipper) are found in transcription regulators.
They increase the strength and specificity of the protein-DNA interaction. |
|
|
