Week 5 Textbook Flashcards
explain briefly what RNA is
ribonucleic acid
produced by transcription of DNA which is usually single stranded
- has covalently linked ribonucleotide subunits
has lots of structural, catalytic and regulatory functions in cells
what is the process called when DNA gets converted into RNA
transcription
- coping the nucleotide sequence of multiple genes into RNA
- copied into another chemical form
- RNA nucleotides = phosphodiester bonds
what is the process when RNA makes a protein
translation
what is the difference between RNA and DNA
ribonucleodies = A, U, G, C
ribose sugar
single stranded
- can also have structural, regulatory and catalytic roles that DNA does not have
T/F RNA has more freedom to move and flexibility rather than DNA
true
single stranded = easier than double stranded = stiff
what is an RNA transcript
the RNA chain produced by transcription - complementary to the template strand - using DNA
- changes all T to U
T/F RNA can only transcribe short lengths of DNA
true
the helix reforms and the RNA is single stranded which makes it copy only a limited amount
what is RNA polymerase
catalyzes the formation of the phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain
unwinding the DNA to expose new regions
RNA chain is elongated one nucleotide at a time in the ___ to ___ direction
5’ to 3’ direction = synthesized but 3’ to 5’ on the parent chain
- ATP is needed to drive the reaction forward
T/F multiple RNA copies can be made from the same gene in a relatively short period of tiem
true
what kind of substrate does RNA polymerase use to link the ribonucleotides
ribonucleoside triphosphates as substrates - doesn’t use deoxyribonucleotides
T/F RNA chain can start without primer
true
does not accurately proofread their work
why are mistakes in RNA not taken seriously
because RNA is not the storage of genetic information in cells
- minor consequences
explain the role of mRNA
messenger RNAs = direct the synthesis of proteins
- carries information transcribed from one gene which codes for a single protein
what are the functions of noncoding RNA
enzymes, structure, and regulatory components for a wide variety of processes in the cell
explain ribosomal RNAs
rRNA
- form the structural and catalytic core of the ribosomes which translate mRNAs into protein
explain tRNA
transfer RNAS
- act as adaptors that select specific amnio acids and hold them in place as ribosome links thems to a growing proteine
explain miRNAs
microRNAS
- small
- serve as key regulators of eukaryotic gene expression
explain siRNAS
small interfering RNAS
- provide protection from viruses and transposable elements
what is gene expression
refers to the process by which the information encoded in a DNA sequence is converted into a product - RNA or protein - this has some effect on the cell of the organism
what is a promotor
a gene region that the RNA polymerase latches onto to begin its process
- it is a DNA sequence that initiates gene transcription - recognized by RNA polymerase and its accessory proteins
- elongation continues until it reaches the second signal in the DNA
what is the terminator (stop site) used for
tells the RNA polymerase to stop at this signal
releases the DNA template and the new RNA transcript is made
- the interaction between the 3’ end of the RNA template that causes the signal to let go of the template DNA
T/F before transcription begins it must only preceded by a promotor
true
in bacteria what is the subunit called that recognizes the promotor seq
sigma factor
these base pairs that make the sequence = unique features on the outside of the helix
- this allows the sigma factor to identify it without having to unwind the DNA
how does RNA know which strand on the DNA to turn into the template strand
both strands have different base pairings and will create different RNA transcripts
- every promotor has polarity - contains 2 different nucleotide sequences in the 5’ to 3’
since RNA polymerase can only synthesize from the 5’ to 3’ direction it can only use the strand that is oriented in the 3’ tp 5’ direction as the template
- in some genes, they use only one strand as the template bc it is determined by the promotor
what are the three polymerases that are in eukaryotes
RNA polymerase 1, 2, 3 = responsible for different types of genes
1 and 3 = transcribe genes that encode tRNA, rRNA and other RNAs that play a structural and catalytic role in the cells
2 = transcribes the rest = all that encode proteins, miRNA, noncoding RNAs (spliceosomes)
t/f transcription in eukaryotes require no other help from proteins
false
- requires assistance
t/f eukaryotic genes are more spaced out than bacteria which enables them to engage in more complex forms of transcriptional regulation
true
what are general transcription factors
these proteins assemble on the promotor where they position the RNA polymerase and pull apart the RNA double helix to expose the template strand for transcription to start
EUKARYOTES
what is the significance of the TATA box
this structure helps to serve as a landmark fo the subsequent assembly of other proteins at the promotor
- used by RNA polymerase 2
- located 30 nucleotides upstream. once the general transcription factor TFIID finds the TATA, the other proteins assemble to form a complete transcription initiation complex
if a polymerase becomes dislodged from the DNA before transcription is complete, what happens
it needs to reinitiate and start the entire process over again starting from a new promotor
what do elongation factors do
they help and allow rna polymerase 2 to move thru the DNA that is packaged into nucleosomes
what happens when RNA polymerase 2 finishes transcribing a gene
it releases from the DNA
the phosphates on its tail are removed by protein phosphatases
- the polymerase finds another area to transcribe via promotor
what direction do the ribsomes attach to the synthesized mRNA in bacteria cells
attach to free 5’ to 3’ of the rna transcripts and begin TRANSLATING into proteins
- bacteria cells = no nucleus to enclose the DNA so they are exposed to cytosol which contains the ribsomes
where does translation take place in eukaryotic cells
in the cytosol outside of the nucleus
- but it needs to be transported out of the nucleus thru the small pores of the nuclear envelope
what steps occur in RNA processing before RNA is transported out the nucleus for translation
rna processing = capping, splicing, polyadenylation = modifications before it becomes a mature mRNA
- this occurs as the RNA Is being synthesized
- they follow along on the phosphorylated tail of polymerase 2
what occurs in the RNA capping process
modifies the 5’ end of the RNA
- adds an atypical nucleotide (Guanine) attached to a methyl group (+ charged)
what happens in the polyadenylation process
provides a newly transcribed mRNA with special structures to the 3’ end
enzyme trims the 3’ end
adds a repeated series of adenine to the trimmed end = poly-Atail = hundred nucleotides long
what does the modification of mRNA do?
capping and poly-Atail = increase stability of the mRNA molecule
- facilitates its export from the nucleus to the cytosol - this marks the molecule as a mRNA specifically
- makes sure in other machinery that both ends of the mrna are present before protein synthesis begins
what are introns and exons
introns = intervening sequences = noncoding sequences
exons = expressed sequences, shorter
what is RNA splicing
introns ar removed from the new strand of RNA and the exons are stitched together
- after cutting, they are modified on both 5’ and 3’ ends = functional mRNA molecule to leave the nucleus
precursor mRNA/pre-mRNA
means the mRNA before it becomes functional
poly-A-tail
Guanine cap
splicing
how does the splicing protein know which parts to remove
the introns contain few short nucleotide sequences that act as cues
- found near the end or the beginning of the intron
what are snRNAs
small nuclear RNAs are packaged with additional proteins to form small nuclear ribonucleoprotein
- they recognize the splice-site sequences through the complementary base pairing
- they form the core of the spliceosome
what is a spliceosome
= a large assembly of RNA and protein molecules that splice introns out of the mRNA
- two splicesomes on either end of the introns. they base pair with the ends. they come together (pair with each other) and close off the loop and one side is cut. the other cut needs to be cut and then the exons need to be put together
what is the alternative splicing
they can be spliced in different ways
- the production of different mRNA and proteins from the same gene by splicing the RNA transcripts in different ways
- allows different proteins to be produced from the same gene
- different combinations of exons can line up and be glued together
what are biomolecular condensates
RNA transcripts are made with lots of help from other proteins (ride on the phosphorylated tail of polymerase)
- they also form loose molecular aggregates = factories for the production of RNA
- brings together all the proteins that help into a dynamic and sub-compartmental unit within the nucleus - held together by weak noncovalent bonds - they don’t need an enclosing membrane to keep the compartments together since they are broken and formed regularly
- this is common in a lot of other processes
how does the functional mRNA transport from the nucleus to the cytosol
- all of the RN debris and introns and enzymes and proteins can be dangerous to the mRNA
- only correct mRNAs are exported - controlled by the nuclear pore complexes which connect the nucleoplasm with the cytosol = gate controlling what goes in and out
- needs to have poly-A-tail, cap, spliced correctly
the debris gets degraded and stays in the nucleus - this is reused for the other transcription
what is the length of time that an mRNA can be functional for protein synthesis
bacterias = 3 mins life span to be reused as many times as it can
eukaryotes = longer, the ones that encode beta-globin have 10 hr life spans
- different lifespans are controlled in the RN called the 3’ untranslated region which is between the 3’ end of the coding sequence and the poly-A-tail
