CH 10: Transcription Flashcards
What is transcription?
copying DNA into RNA
How does replication differ from transcription?
ex. enzymes, direction, primers, template, initiation
replication - DNA pol, 5’-3’, primers present, both strands are templates, begins at origins
transcription - RNA pol, 5’-3’, no primers needed, 1 strand template, starts at promoters
What is a ribozyme and why is this so special?
a catalytic RNA, can catalyze rxns even though its made of RNA not protein - pointed to RNA being the original genetic material
Primary vs Secondary RNA structure, what is RNA?
RNA - polymer of nucleotides, has sugar, phosphate group, and nitrogenous base joined by phosphodiester bonds, AUGC
primary - nucleotide bases
secondary - RNA folds, hydrogen bonds between complementary bases on folded strand
while DNA is a double helix secondary structure, RNA can be various types of structures
RNA has 2’-OH group
What are mRNA, rRNA, tRNA?
mRNA - messenger, coding instructions for polypeptide chain from DNA to ribosome
rRNA - ribosomal, structural component of the ribosome
tRNA - transfer, links mRNA coding sequence to 3 pair nucleotide that codes for an amino acid
3 major component of transcription?
- DNA template
- RNTPs, raw materials
- transcription apparatus - extra proteins for transcription to occur
All cellular RNAs are synthesized from ? through the process of transcription.
DNA templates
only individual genes that are needed are transcribed
What is the template strand in transcription?
nucleotide DNA strand that is used as a template during transcription
RNA synthesized during transcription is complementary and antiparallel to the DNA template strand
What is the transcription unit?
sequence of nucleotides in DNA that encodes a single RNA molecule
sequences necessary for transcription has:
1. promoter
2. RNA-coding sequence
3. terminator.
What shape do DNA molecules take under transcription?
Christmas tree - RNA molecules come out vertically while being transcribed from DNA
RNA molecules are made in what direction? Characteristics of RNA synthesis?
5’-3- direction, complementary and antiparallel to the DNA template strand
What purpose do rNTPs (ribonucleoside triphosphates) serve in initiation?
rNTPS are added to the 3’-OH group of the growing RNA molecule
RNA does not require a primer but a promoter
The transcription apparatus refers to a complex of proteins and enzymes that facilitate transcription.
What is the special function of bacterial RNA polymerase? What is the core enzyme and sigma factor?
bacteria only has one type of RNA polymerase that starts up synthesis of supporting RNAs (m/t/rRNA)
five subunits make up the core enzyme of bacterial RNA pol
sigma factor - another RNA pol subunit that binds to promoter when transcription starts (E. coli)
Eukaryotic RNA polymerase I, II, III are responsible for transcribing different classes of RNA.
I - large rRNA, large ribosomal RNA
II - pre-mRNA
III - tRNA, small rRNA, involved in regulation
Transcription is broken into ?
- Initiation - transcription apparatus assembles on the promoter and begins the synthesis of RNA
- Elongation - DNA is threaded through RNA polymerase and the polymerase unwinds the DNA and adds new nucleotides, one at a time, to the end of the growing RNA strand
- Termination - recognition of the end of the transcription unit and the separation of the RNA molecule from the DNA template
What are consensus sequences and why are they important in bacteria? What are the most common consensus sequences found in all bacterial promoters?
most commonly encountered nucleotides at each site in a group of related sequences, implies seq has important function
consensus sequences TTGACA at -25 and TATAAT (Pribnow box) at -10
Since no primers are needed for initiation, the location of the consensus seq helps …
determine the position of the start site and helps RNA pol recognize the start site
Bacterial transcription taken care of by RNA pol… what does RNA pol bind to in order to initiate transcription? What complex is formed once RNA binds to _____ ?
RNA pol binds to the sigma factor
RNA pol and sigma factor for a complex known as holoenzyme - binds to consensus seq and then entire promoter
Elongation carried out by ?
RNA polymerase
Transcription stops after the terminator has been transcribed. What are the two major types of bacterial terminators?
Rho-dependent - uses rho factor
Rho-independent - doesn’t use rho factor, hairpin structure formed by inverted repeats followed by UUUUUUU
For genes that have rho-dependent terminators, there is a special site called the _____ site. What happens when RNA pol reaches a terminator site?
rut site - rho factor binds to rut site behind RNA pol
once terminator site is reached by RNA pol, RNA pol pauses and the bound rho factor catches up and uses helicase activity to unwind DNA-RNA and halt transcription
Rho independent termination in bacteria is a _____ process
multistep
transcription halts when inverted repeats form a hairpin followed by a string of UUUUUUU
Where does transcription and translation happen in eukaryotic vs prokaryotic cells?
prok - coupled, happen at same time
euk - transcription (nucleus) translation (cytoplasm)
What is colinearity and how do we see it in euk vs prok cells?
colinearity - refers to that number of nucleotides in a gene is proportionate to the amino acids in the protein
eukaryotes - noncolinear with proteins, there are coding (exons) and noncoding sections (called introns) of the DNA compared to mRNA
bacterial genes/ prokaryotes - colinear with proteins
Monocistronic vs polycistronic
monocistronic - euk cells, each gene is encoded by a different specific promoter, so when each gene is transcribed to mRNA, new promoter was used for each mRNA section
polycistronic - prok cells, one promoter is used to one entire mRNA strand transcribed from DNA (which has many genes) to create more than one protein
Eukaryotic genes contain both _____ and _____. They are both _____ into RNA but ? are later removed by RNA processing or ?. Are introns present in bacterial genes?
introns and exons, transcribed, introns, splicing
no
What is the gene made of?
all DNA sequences - exons and introns
5’ and 3’ UTR (untranslated regions that are important for translation)
transcription unit - promoter, RNA coding seq, terminator
What is the function of mRNA?
serves as a template for protein synthesis, takes complementary DNA sequence and goes to ribosome where it will be read by tRNA to start building polypeptide chain
each three nucleotide bases on mRNA codes for ? which make up ?
these three nucleotides that code for amino acids are known as ?
amino acids, proteins
codons
Mature mRNA has three regions, what are they? Why are the 5’ and 3’ UTS regions important if they don’t code for amino acids of proteins?
What is the Shine-Dalgarno sequence?
5’ UTR, protein coding region, 3’ UTR
5’ and 3’ UTR have important info for RNA stability and regulation of translation
Shine-Dalgarno - consensus seq in prok, recognition site of ribosome so it can start translation
premRNA processing: What do we do to the 5’ and 3’ ends of the mRNA?
add an extra guanine nucleotide and additional methyl groups to the 5’ end of the mRNA - make 7-methylguanosine, this group attaches with a special 5’-5’ bond
add a bunch of adenine nucleotides to 3’ end of mRNA, helps ribosome attach
What are all of the post transcriptional modifications to eukaryotic premRNA?
5’ cap - stability
3’ poly-A tail - helps ribosome attach
RNA splicing - remove noncoding introns
RNA splicing happens in the _____, specifically in the _____. The three important consensus sequences are the 5’, 3’, and branch point. What are the important nucleotide markers of each?
nucleus
5’ - start with GU
3’ - end with AG
branch point - special adenine
*need all 3 sequences for splicing to occur
Splicing of premRNA has two main steps. They happen within the _____ which again is in the _____.
- 5’ end of intron cut from upstream (first) exon and connected to branch point to form lariat
- 3’ end of intron cut from downstream (end) exon and then the ends of the two exons are merged together
Alternative processing pathways allow for various ways of processing premRNA to produce alternate mRNA types.
What is alternative splicing?
same premRNA can be spliced in different ways to create different mRNA strands
these strands are then translated into different (a.a seq) proteins
this is bc there are many different 3’ cleavage sites in premRNA
What is tRNA and what is the shape of it? What is the anticodon? What special RNA nucleotide bases does tRNA have?
tRNA attaches to a specific amino acid and carries it to the ribosome to add to growing polypeptide chain
cloverleaf shape
anticodon - three nucleotide seq that pairs with mRNA codon to make sure amino acids link in right order during translation
ribothymine and pseudoridine
Prokaryotic vs Eukaryotic characteristics during transcription
prok - polycistronic, coupled transcription translation, promoter, 1 RNA polymerase, sigma factor, Shine-Dalgamo seq
euk - monocistronic, transcription - nucleus, translation - cytoplasm, premRNA processing, promoter, RNA pol I - large rRNAs, RNA pol II - mRNA, RNA pol III - tRNA+small rRNA, transcription factors
How do antibiotics target bacteria?
antibiotics target parts of bacterial ribosomes that differ from human eukaryotic cells or ribosomes
What is RNA interference? What do small interfering RNAs and microRNAs do? What is RISC?
a euk power that limits invasion of viruses, blocks expression of their genes
siRNAs - targets mRNA for degradation
microRNA - blocks translation
*both are made from double stranded RNAs
siRNA and microRNAs combine with proteins to form RNA induced silencing complex (RISC) - which cleaves mRNA and can lead to degradation or blocking translation of mRNA
***** slide 51
What do piwi-interacting RNAs do?
inhibit transposons - DNA seq that can move around, can cause mutations, alter gene expression, etc.
CRISPR RNAs are only found in porkaryotes. What do they do?
defense mechanism against foreign DNA
