Chapter 7 Flashcards
1
Q
How Cells Read the Genome
A
- even before DNA code was uncovered, we knew that the info contained in genes directs the synthesis of proteins
- proteins determine cell structure and function
- each type of protein has its own unique amino acid sequence, which dictates how the chain will fold to form a molecule with a distinctive shape and chemistry
- The genetic instructions carried by DNA must therefore specify the amino acid sequences of proteins
2
Q
gene
A
- When a particular protein is needed by the cell, the nucleotide sequence of the appropriate segment of a DNA molecule is first copied into another type of nucleic acid—RNA (ribonucleic acid)
- the segment of DNA is the gene
- resulting RNA copies are used to direct synthesis of the protein
- genetic info in cells: DNA to RNA to protein
- occurs in ALL cells(central dogma)
3
Q
transcription and translation
A
- how cells read out/express the instructions in their genes
- many identical RNA copies come from the same gene
- each RNA molec can direct the synthesis of many identical protein molecs
- cells can rapidly synthesize large amts of protein
- BUT each gene can be transcribed, and its RNA translated, at different rates, providing the cell with a way to make vast quantities of some proteins and tiny quantities of others
- a cell can change (or regulate) the expression of each of its genes according to the needs of the moment
4
Q
transcription
A
- The first step a cell takes in expressing one of its many thousands of genes is to copy the nucleotide sequence of that gene into RNA
- called transcription bc language(nucleotides) is same
- Steps:
- small portion of DNA double helix opens and unwindes to expose bases on each strand
- one of 2 strands is template for RNA synthesis
- Ribonucleotides are added, one by one, to the growing RNA chain(complementary base pairing)
- enzyme RNA polymerase links ribonucleotides to RNA chain using covalent bonds
- RNA chain produced by transcription (RNA transcript)
- exactly complementary to DNA strand
5
Q
RNA
A
- a linear polymer made of four different nucleotide subunits, linked together by phosphodiester bonds.
- all RNA is made transcription
6
Q
DNA vs RNA
A
- the nucleotides in RNA are ribonulcleotides(they contain ribose) while DNA contains deoxyribose
- DNA has bases ACTG; RNA has ACUG
- DNA is double stranded(can’t fold), RNA single stranded(can fold into shapes like polypeptide chains fold up to form final protein shapes)
- SO, DNA functions as an info store, but some RNAs have structural, regulatory, or catalytic roles
*Both have their nucleotides linked by a phosphodiester bond
7
Q
DNA replication vs transcription
A
- newly formed DNA strands remain H-bonded to DNA template strand, but just behind where the ribonucleotides are added, the RNA chain is displaced and double helix re-forms
- this is why RNA is single stranded
- RNA are copied from a limited region of DNA so RNA is much shorter than DNA
- DNA in human chromosomes is up to 250 million nucleotide pairs long, RNA is roughly a couple thousand nucleotides or less
8
Q
RNA polymerases
A
- catalyze the formation of the phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain
- The RNA polymerase moves stepwise along the DNA, unwinding the DNA helix just ahead to expose a new region of the template strand for complementary base-pairing
- RNA chain is extended one nucleotide at a time from 5’ to 3’
- The incoming ribonucleoside triphosphates (ATP, CTP, UTP, and GTP) provide the energy needed to drive the reaction forward
- the synthesis of the next RNA is usually started before the first RNA has been completed b/c RNA is released from DNA almost immediately
9
Q
DNA polymerase vs. RNA polymerase
A
- RNA polymerase uses ribonucleoside for phosphates as substrates, so it catalyzes the linkage of ribonucleotides, not deoxyribonucleotides
- unlike DNA polymerase, RNA polymerases can start an RNA chain w/o a primer
- This difference likely evolved because transcription need not be as accurate as DNA replication; unlike DNA, RNA is not used as the permanent storage form of genetic information in cells, so mistakes in RNA transcripts have relatively minor consequences for a cell
- RNA polymerase makes one mistake every 104 nucleotides copied into RNA, while DNA makes only one mistake for every 107 nucleotides copied
10
Q
message RNA(mRNA)
A
- The vast majority of genes carried in a cell’s DNA specify the amino acid sequences of proteins.
- The RNA molecules encoded by these genes—which ultimately direct the synthesis of proteins
- In eukaryotes, each mRNA typically carries information transcribed from just one gene, which codes for a single protein
- in bacteria, a set of adjacent genes is often transcribed as a single mRNA, which therefore carries the information for several different proteins.
11
Q
non messeneger RNA
A
- the final product of other genes is RNA itself
- these non messenger RNAs, like proteins, have various roles: reulatory, structural, and catalytic cell components
- they play ket parts in translating genetic message into protein
- ribosomal RNA(rRNA) form the structural and catalytic core of the ribosomesm which translate mRNAs into protein
- transfer RNA(tRNA) act as adaptors that select specific amino acids and hold them in place on a ribosome for their incorporation into protein
- microRNAs(miRNA) serve as kept regulators of eukaryotic gene expression
12
Q
gene expression
A
- the process by which the information encoded in a DNA sequence is translated into a product that has some effect on a cell or organism.
- When final product of the gene is a protein, gene expression includes both transcription and translation.
- When an RNA molecule is the gene’s final product, however, gene expression only requires transcription.
13
Q
signals in DNA tell rNA polymerase Where to start and finish transcription
A
- is the main point at which the cell selects which proteins or RNAs are to be produced. To begin transcription, RNA polymerase must be able to recognize the start of a gene and bind firmly to the DNA at this site
- In Bacteria:
- When an RNA polymerase collides randomly with a DNA molecule, the enzyme sticks weakly to the double helix and then slides rapidly along its lengt
- RNA polymerase latches on tightly only after it has encountered a gene region called a promoter(specific sequence of nucleotides that lies immediately upstream of the starting point for RNA synthesis)
- RNAp opens up double helix in front of promoter
- one strand is template for complementary base pairing with incoming ribonucleoside triphosphates, two of which are joined together by the p to begin synthesis of RNA chain
- elongation continues until enzyme encounters the terminator(stop site)(terminator sequence is contained within the gene and is transcriber into the 3’ end of new RNA)
14
Q
sigma(σ)factor
A
- used in bacteria
- a subunit of RNAp that recognizes promoter on DNA
- It turns out that each base presents unique features to the outside of the double helix, allowing the sigma factor to find the promoter sequence without having to separate the entwined DNA strands
15
Q
Choosing which of the 2 DNA strands is template
A
- each strand has a different nucleotide sequence and would produce a different RNA transcript
- Every promoter has a certain polarity: it contains two different nucleotide sequences upstream of the transcriptional start site that position the RNA polymerase, ensuring that it binds to the promoter in only one orientation
- Because the polymerase can only synthesize RNA in the 5′-to-3′ direction once the enzyme is bound it must use the DNA strand oriented in the 3′-to-5′ direction as its template
- on a given chromosome, transcription DOESN’T always proceeds in the same direction. With respect to the chromosome as a whole, the direction of transcription varies from gene to gene
16
Q
how Eukaryotic gene transcription differs from bacterial
A
- bacteria has 1 type of RNAp, eukaryotic has 3: RNAp I,II,III
- these RNAps each transcribe diff types of genes
- I and III transcribe the genes encoding tRNA, rRNA, and other RNAs that play structural and catalytic role
- II transcribes majority of eukaryotic genes, including those that encode proteins and miRNAs
- bacterial RNA polymerase w/ sigma subunit is able to initiate transcription on its own, BUT eukaryotic RNAp requires help from accessory proteins(mainly general transcription factors which assemble at each promoter w/ RNAp to begin transcription)
- in bacteria, genes are close together in DNA, but in eukaryotes, genes are spread out w/ stretches of up to 100,000 nucleotides btwn each gene which allows a single gene to be controlled by a large variety of regulatory DNA sequences scattered along the DNA
- eukaryotic is more complex than bacteria
- eukaryotic transcription initiation must take into account the packing of DNA into nucleosomes and more compact forms of chromatin structur
17
Q
general transcription factors
A
- These accessory proteins assemble on the promoter, where they position the RNAp and pull apart the DNA double helix to expose the template strand, allowing the p to begin transcription
- similar to sigma factor in bacterial transcription
- TFIIB, TFIID, etc.
18
Q
assembly process of general transcription factors
A
- general transcription factor TFIID binds to a short segment of DNA double helix of mostly T and As
- (this part of promoter is TATA box)
- TATA box is usually 25 nucleotides upstream of start site
- local distortion of DNA double helix occurs, which other proteins use as a landmark
- other factors assemble w/ RNAp to form a complete transcription complex
- order of assembly differs from 1 promoter to next
- phosphate groups are added to RNAp “tail” so RNAp can be released and transcription can start
- TFIIH(contains protein kinase as a subunit) initiates liberation
- when transcription begins, general transcription factors release from DNA
- when RNApII finishes transcription it is released from DNA, the phosphates on tail are stripped off by protein phosphates, and RNApII finds a new promoter
- Only the dephosphorylated form of RNA polymerase II can initiate RNA synthesis
19
Q
eukaryotic mrNAs Are processed in the Nucleus
A
- bacterial DNA lies exposed to the cytoplasm, which contains ribosomes on which protein synthesis occurs
- as mRNA in bacterium are being synthesized, ribosomes attach to free 5’ end of RNA transcript and begin translating it into protein
- in eukaryotic cells, DNA is within nucleus
- transcription=in nucleus
- protein synthesis=on ribosomes in cytoplasm
- mRNA must be transported out of nucleus throguh small pores in nuclear envelope
- RNA processing occurs(capping, splicing, polyadenylation)
- enzymes responsible for RNA processing ride on phosphorylated tail of RNApII as it synthesizes RNA and they process the transcript as it emerges from the polymerase
20
Q
RNA capping
A
- occurs only on RNA transcripts destined to become mRNA molec(precursor mRNAs/pre-mRNAs)
- capping modifies 5’end which is synthesized first
- an atypical nueclotide(guanine bearing a methyl group) is attached to 5’ end by triphosphate bridge
- occurs after RNApII produced about 25 nucleotides of RNA, long before the whole gene has been transcribed
21
Q
Polyadenylation
A
- adds special structure on newly transcribed mRNAs 3’
- trimmed by an enzyme that cuts RNA chain at a particular sequence of nucleotides
- transcript is then finished by a 2nd enzyme that adds a series of repeated adenines to cut end
- poly-A tail is usually a few 100 nucleotides long
22
Q
Effect of capping and polyadenylation
A
- increase stability of eukaryotic mRNA molec
- facilitate its export from nucleus to cytoplasm
- generally mark the RNA molec as an mRNA
- used by protein-synthesis machinery to make sure both ends of mRNA are present and that message is complete before protein synthesis begins
23
Q
Introns
A
- pre-mRNAs undergo extra processing before they are functioning mRNAs
- far more drastic than capping+polyadenylation
- in bacteria, most proteins are encoded by uninterrupted stretches of DNA sequence that is transcribed into an mRNA that, w/o further processing, can b translated into protein
- in eukaryotes, most protein coding genes are interrupted by introns(long, noncoding, intervening sequences~range from 1-10,000 nucleotides long)
- exons: expressed sequences(scattered pieces of coding sequence) are shorter than introns and are a small fraction of whole gene
- some protein-coding eukaryotic genes lack introns, some have few, but most have many
- exons: expressed sequences(scattered pieces of coding sequence) are shorter than introns and are a small fraction of whole gene
