Chapter 15 Flashcards
Briefly discuss the contributions of the following individuals in terms of our understanding of how genes work (don’t have to understand the actual experiments – just their conclusions).
- Garrod
- Beadle and Tatum
Garrod
First to connect diseases with inheritance. Defective gene produces a defective enzyme.(by looking at the family map)
Beadle and Tatum
Developed one gene - one enzyme hypothesis = each gene dictates production of a specific enzyme
( Experimental evidence. Looked at bread mold)
What is the one gene – one polypeptide hypothesis? Know that only a very small fraction of human DNA encodes for polypeptides
One gene - one polypeptide hypothesis is that one type of enzyme makes one type of protein. Only about 1% of human DNA is exons which codes for proteins.
What is the “central dogma” of molecular biology? What is transcription? Translation? Know where in the cell these events take place for both prokaryotic and eukaryotic cells.
Central dogma is a process in which DNA code is converted into RNA to protein (which determines the phenotype like a blue eye)
Transcription : DNA –> RNA (in the nucleus)
Translation: RNA –> protein (in the cytoplasm)
- both happens in cytoplasm for prokaryotes`
Understand how DNA is an information storage molecule. Which type of RNA contains the “code” for polypeptides?
mRNA
Review the main differences between RNA and DNA. What are the main similarities?
Differences : pentose sugar (ribose for RNA, deoxyribose for DNA), strand (RNA is single-stranded, DNA is double stranded), bases (RNA – Uracil, DNA – Thymine)
Similarities : both have pentose sugar, phosphate-sugar backbone
What is a promoter? Know the “boxes” necessary for RNA polymerase to recognize and bind to the prokaryotic promoter. Understand the meaning of the terms “upstream” and “downstream” in regards to DNA.
Promotor : sequence of DNA where protein bind and initiate transcription.
-10 box, -35 box
Upstream : against the direction of transcription
Downstream : along the direction of transcription
What is a consensus sequence? How does the relationship to the consensus sequence relate to the strength of the promoter?
Consensus sequence : most frequent sequence of DNA, statistically most likely to see particular sequence in particular locations ( TATATT at -10 region)
Closer the promotor is to the consensus sequence; stronger the promotor is. (=easier to load RNA polymerase)
In prokaryotic transcription, what is meant by “-10 box” and -35 box”? Where (distance and location) does transcription begin in relationship to the “boxes” mentioned above? Which strand of DNA is the template strand? Which strand of DNA is the coding strand?
Transcription start at +1.
-35 box = 35 micrometer upstream from transcription start site
Template strand : where transcription(always made in 5’ to 3’ direction) occurs.
Coding strand : opposite of template strand.
What is the role of the sigma (s) subunit in transcription? Regarding RNA polymerase, what is the difference between the core enzyme and the holoenzyme? What part of the DNA does sigma factor bind?
Sigma factor binds to RNA polymerase to make holoenzyme - sigma factor recognizes promotor and bring the core enzyme to the active site for transcription to start. Core enzyme cannot recognize the promotor alone. Sigma factor binds to the promotor region (from -10 box to -35 box), putting its active site at +1.
What is “promoter clearance’’? What happens to the structure of the RNA polymerase once sigma factor “leaves”? How does this relate to the start of elongation?
Promotor clearance is test run to make sure the transcription works, it creates short abortive RNA transcripts –> afterwards sigma factor dissociates. –> causes RNA polymerase to clamp around the strand.
Promotor not sticking to the promotor, so it can start to elongate.
In prokaryotic cells, know that translation occurs before transcription finishes (polyribosome). Why is this NOT the case in eukaryotic cells?
Because transcription in eukaryotic cell occurs in the nucleus and needs further processing to go into cytoplasm where translation occurs.
How many different RNA polymerases are found in prokaryotic cells? in eukaryotic cells? What are the MAIN classes of RNA that these different polymerases transcribe in eukaryotic cells?
1 type of RNA polymerase in prokaryotic cells,
3 different RNA polymerase in eukaryotic cells.
- RNA polymerase I : most rRNA genes
- RNA polymerase II : mRNA (all protein-coding genes)
- RNA polymerase III : tRNA and small RNAs
In eukaryotic cells, what is meant by the terms “core promoter”? What is a TATA box?
Core promotor in eukaryotic cells are the region of DNA where RNA polymerase II binds. TATA box is part of core promotor sequence about 25 nucleotides upstream the active site.
How does initiation of transcription differ in prokaryotic and eukaryotic cells?
- In prokaryotic cells, RNA polymerase recognizes and binds to the promotor with sigma factor.
- In eukaryotic cells, transcription factors (TF) bind to the core promotor which than allows for RNA polymerase and other TFIIs to bind.
What is the role of the general transcription factors in eukaryotic transcription? What is the role of TFIID? What is the transcription initiation complex?
TFIID recognizes and binds to TATA box.
Transcription initiation complex is made up of RNA polymerase II and TFIIs - it initiates transcription
In eukaryotes what is the difference between a primary transcript and a mature transcript? Understand the types of post-transcriptional modifications (also known as mRNA processing) of a mRNA molecule in eukaryotes. Where and when do these modifications occur? What is a 5’ cap? A polyA tail?
Primary transcript of eukaryotes includes exons and introns(non-coding regions)
Mature transcript is processed with intron splicing, poly-A-tail, and 5’cap. These modifications occur inside the nucleus. Capping enzyme catalyze the 5’ cap when growing mRNA emerges. Intron splicing can happen during or after transcription. Poly A tail can only add to end once the transcription is over.
5’ cap is upside-down modified guanine attached to 5’ end of initial RNA transcript (which still holds nucleotide triphosphate.
Poly-A-tail is repeated units of AAAA’s(adenosine base repeats) - by polyadenylation factors
- Understand the role of phosphorylation of the C-terminal domain (CTD) of RNA polymerase II in RNA processing. What is the purpose of this phosphorylation? What enzyme phosphorylates the CTD?
TFIIH, acting as kinase, puts phosphate on the C terminus domain (CTD) –> becomes binding site for enzymes like capping factors, splicing factors, and polyadenylation factors.
