Textbook 1.3 Flashcards
pg. 473-478, 381 - 383, 531-534 pg. 406-413, 417-429
Dispersed chromatin
associated with interphase activity of cell (replication and transcription)
When is chromatin in its most condensed state
In a mitotic cell—facilitates delivery of DNA to daughter cell.
Telomere sequence
TTAGGG (complementary strand is AATCCC) repeated about 500 to 5000 times
Which strand overhangs after DNA replication and what is done with it
3’ end overhangs because primer is removed leaving empty space on 5’ end of DNA. Overhanging strand is tucked back into double stranded portion of telomere.
Telomerase
A reverse transcriptase that uses an RNA template to synthesize DNA. Adds repeat units to 3’ end which serves as a template for a conventional DNA polymerase to add to 5’ end. Actually contains RNA.
Function of telomeres
- protect chromosomes from nucleases
- prevent ends of chromosomes from fusing with each other
Why do telomeres shrink?
Because most cells lack telomerase. When telomere shortening reaches a critical point, cell stops dividing.
Which cells contain telomerase?
germ cells of gonads, stem cells, and 90% of human tumours.
Topoisomerases
Relax supercoiled DNA strands. One cuts through a single strand and the other cuts through the whole duplex.
Human genome
Equivalent to all the genetic information that is present in a single (haploid) set of human chromosomes (22 autosomes and sex chromosomes).
Denatured DNA strands absorb…
more UV radiation
Melting temp corresponds to
half the shift towards increased UV radiation. More G and C means higher melting temp.
Difference between NER and BER
Nucleotide excision repair removes a whole sequence of nucleotides which is then filled in by DNA polymerase and sealed by ligase while Base ER removes single altered nucleotides.
Which bond does DNA glycosylase cleave?
The glycosidic bond between the sugar and the base
Difference between MMR in eukaryotes and E. coli
Mismatch repair in eukaryotes recognizes the nicks in the newly synthesized strand while in E. coli a protein looks for methylated adenines
RNA polymerases in eukaryotes vs prokaryotes
Even the simplest euk. have three types of RNAPs while prok.s have one.
Difference in transcription between euk. and prok.
Euk. require many accessory proteins called transcription factors
RNA polymerase in E. coli
E. coli contains a single type of RNAp composed of 5 subunits which associate to form a core enzyme
Function of sigma factor
Increases RNAps affinity for promoter sites while decreasing affinity for DNA in general (allows whole complex to slide along DNA until promoter region is reached).
The nucleotide at which transcription is initiated is denoted as…and the one right before is…
- +1
- -1 (upstream)
Promoters
sites of DNA that bind RNAp
What happens to the sigma factor after the RNAp enzyme has been transformed into a transcriptional elongation complex?
After ten ish nucleotides have been successfully transcribed, enzyme undergoes conformational change and sigma factor is released.
consensus sequence
TTGACA
sequence that is found 35 bp upstream initiation site of many bacterial genes
-10 bp upstream from initiation is also important
Protein required for termination of bacterial transcription (half the time)? How is termination achieved otherwise?
- Rho, a ring shaped protein
- RNAp stops transcription when it reaches terminator sequence
Primary transcript/Pre-RNA
Initial precursor RNA that leads to all major forms of Euk. RNAs—mRNA, rRNA, and tRNA. Equivalent in length to full length of DNA transcribed. Usually transient as they are processed quickly.
Gene expression
production of a functional product (ex. an enzyme) from a stretch of DNA
mRNA
messenger RNA
coding RNA that creates a complementary strand to section of DNA that can be used to produce polypeptide. Allows huge DNA molecule to stay in nucleus while smaller RNA molecule with genetic info copied can pass into cytoplasm.
Where are proteins synthesized
in the cytoplasm
Ribosomes contain both…
RNA and protein.
Ribosomes
participate in protein translation
rRNA
ribosomal RNA
Does not function in an informational capacity, rather provides structural support for ribosome and helps catalyze chemical reaction in which amino acids are covalently linked to one another.
tRNA
Transfer RNA
translate info in mRNA nucleotide code into amino acid sequence (polypeptide)
What is RNA folding driven by?
Formation of regions of complementary base pairs. Base-paired regions form double stranded stems which connect to single stranded loops.
Difference between RNA and DNA base pairing
RNA base pairing is MUCH less discriminatory—contains non standard base pairs which serve as recognition sites for proteins and other RNAs.
Do Euk. and Prok. have different RNAp?
No, RNA polymerase is same in both.
Function of RNAp
enzymes that incorporates nucleotides into strand of RNA that is complementary to template DNA.
Which direction does RNAp move along template strand
3’ to 5’, synthesizing a 5’ to 3’ strand
How does RNAp link nucleotides together
Catalyzes highly favourable reaction in which ribonucleoside triphosphates are cleaved into nucleoside monophosphates as they are polymerized into covalent chain.
What happens to the pyrophosphate produced in polymer reaction of RNA synthesis?
Because the nucleotide incorporation reaction MUST be essentially irreversible, the pyrophosphate (PP) produced in first rxn is hydrolyzed into inorganic phosphate, releasing a large amount of free energy.
All Euk. mRNA precursors are synthesized by…
RNA polymerase II
Promoter sequence for Euk. transcription
TATA box
First step in assembly of preinitiation complex
TATA-binding protein (TBP) (which is part of TFIID) recognizes TATA box and inserts itself into minor groove
CTD of RNAp II
Consists of a sequence of seven amino acids that is repeated over and over (7 times in yeast 52 times in humans)
What part of the RNAp II is modified between the pre-initiation complex and the actually transcription enzyme
RNAp is phosphorylated and the chemical activity is localized in the CTD.
Kinase
a specific enzyme that catalyses the addition of a phosphate group onto a substrate
Function of TFIIH
Phosphorylates serine at position 5 in the CTD repeat peptide
What do phosphorylated sites on the CTD provide?
Sites for proteins involved in RNA processing to bind to ex. 5’ cap formation
Difference between EUk. and bacterial RNAp II transcription termination?
There is no identified termination sequence in Euk. 3’ end of bacterial sequence is generated simply by termination of transcription while in Euk. transcription goes far beyond where the 3’ end will eventually be suggesting a series of processing steps in Euk. transcription termination.
Properties mRNAs share
- Contain a continuous sequence of nucleotides encoding a specific polypeptide 2. They are found in the cytoplasm
- They are attached to ribosomes when they are translated
- Most mRNAs contain a significant noncoding segment (regions at both 5’ and 3’ end)
- Eukaryotic mRNAs have special modifications—poly A tail on the 3’ end (50 to 250 adenosine residues) and a 5’ methylated guanosine cap.
What’s at the junction of exon-intron sites in Euk.?
conserved gene sequence
Difference between prok. and euk. transcription?
Euk. have three types of RNA polymerase and Prok. have only one. Transcription and translation can occur at same time.
