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BIOL 2120 Chapter 17
Terms in this set (139)
Which of the following features is a significant difference in the function of DNA polymerases versus RNA polymerases? See Section 17.1
RNA polymerase does not require a primer to add new nucleotides.
What is the function of the sigma subunit of RNA polymerase in bacterial transcription? See Section 17.1
Sigma is the portion of the enzyme that recognizes specific sequences in the promoter. Without sigma, RNA polymerase can bind to any sequence of DNA.
What is the process called that converts the genetic information stored in DNA to an RNA copy?
Transcription. DNA is transcribed to give an RNA copy.
In _, RNA polymerase produces and RNA molecule with a base sequence complementary to the base sequence of the DNA template strand
Transcription begins at a promoter. What is a promoter?
A site in DNA that recruits the RNA Polymerase. This is the site where the RNA polymerase must bind to initiate transcription.
Which of the following statements best describes the promoter of a protein-coding gene?
The promoter is a nontranscribed region of a gene. The promoter is the regulatory region of a protein-coding gene at which RNA polymerase must bind to initiate transcription—it is not transcribed into the RNA.
What determines which base is to be added to an RNA strand during transcription?
Base pairing between the DNA template strand and the RNA nucleotides. Transcription involves the formation of an RNA strand that is complementary to the DNA template strand.
Which of the following terms best describes the relationship between the newly synthesized RNA molecule and the DNA template strand?
Because the template strand determines the nucleotides to be added to the RNA strand, using the same complementary rules of the DNA, they will be complementary to each other.
What happens to RNA polymerase II after it has completed transcription of a gene?
It is free to bind to another promoter and begin transcription. The enzyme is free to transcribe other genes in the cell.
In eukaryotes, the size of the primary transcript is generally ________ the gene in the template DNA strand. See Section 17.2
The same length. The primary transcript is an exact RNA copy of the DNA coding sequence. **not in mature mRNA form until the primary gets introns spliced off, primary is fresh and unedited, identical to DNA
In addition to splicing, additional modifications at the 5' and 3' end are required to generate a mature mRNA. What is the significance of these modifications? See Section 17.2
These modifications allow the mRNA to be recognized by the protein synthesis machinery and protect it from degradation. The 5' cap and poly-A tail added to pre-mRNA complete the transformation to mature mRNA.
As a result of splicing, most protein-coding genes can encode ______ protein. See Section 17.2
more than one. This allows one gene to code for different mRNAs.
Why is it that bacterial ribosomes can begin translation before mRNA synthesis is completed, but eukaryotic ribosomes cannot? See Section 17.3
In prokaryotes, transcription and translation take place in the cytoplasm. Prokaryotic cells lack a nuclear envelope.
What kind of molecule is the "adapter" that couples amino acid sequences to the sequence of bases in the mRNA? See Section 17.4
RNA. tRNA transfers amino acids from RNA to the lengthening polypeptide chain.
What is the reaction catalyzed by aminoacyl-tRNA synthetases? See Section 17.4
These enzymes catalyze formation of the bonds between the tRNA and the appropriate amino acids. This is known as "charging" a tRNA.
An aminoacyl-tRNA that enters the A site of the ribosome will next occupy which site? See Section 17.5
P site. P stands for "peptidyl" and is in the middle in the ribosome.
How does the arrival of a termination codon at the A site trigger the end of protein synthesis? See Section 17.5
A protein release factor binds in the A site and releases the polypeptide from the final tRNA to which it is bound.After polypeptide release the ribosome dissociates.
The cell uses three different types of RNAs to build proteins. rRNA is part of the ribosome, which is the site of protein synthesis. mRNA carries the genetic information from the DNA; the information specifies the sequence of amino acids in the new protein. tRNA interprets the information from the mRNA and brings the appropriate amino acids to the ribosome.
Contains anticodon and has amino acids covalently attached
Contains exons and specifies the amino acid sequence for a protein
Is a component of ribosomes and is the most abundant form of RNA
Indicate at which step of the replication-transcription-translation process each type of RNA first plays a role.
During which step of the replication-transcription-translation process does each type of RNA first play a role? Drag each item to the appropriate bin. (Not every bin has to be filled.)
Translation/RNA processing- mRNA
Translation- rRNA tRNA
During replication, a faithful copy of a DNA molecule is made.
During transcription, the DNA "message" is copied onto a molecule of mRNA.
During translation, the information carried in the mRNA is transferred to molecules of tRNA to build a protein on the ribosomes.
What enzyme catalyzes the attachment of an amino acid to tRNA?
The tRNA anticodon, GAC, is complementary to the mRNA codon with the sequence _____.
The initiator tRNA attaches at the ribosome's _____ site.
The initiator tRNA attaches to the ribosome's P site.
DNA does not store the information to synthesize which of the following?
Synthesis of organelles is not directly coded in the DNA.
_ begins transcription by binding to promoter sequences in DNA with the help of other proteins
In _, this binding accomplished by protein called sigma. Sigma associates with RNA polymerase and then recognizes particular sequences within promoters that are centered 10 bases and 35 bases upstream from where transcription begins
Eukaryotic promoters vary _ than bacterial promoters
In eukaryotes, transcription begins when a large array of proteins called _ _ _ bind to a promoter. In response, RNA polymerase binds to the site.
Basal transcription factors
In bacteria and eukaryotes, RNA elongates in a _ direction
5' -> 3'
Transcription in bacteria ends when a _ structure forms in the transcribed RNA; in eukaryotes, transcription terminates after the RNA is cleaved downstream of the _ signal.
In eukaryotes, the primary (initial) transcript must be processed to produce a mature RNA
Splicing of primary transcripts removes stretches of RNA called introns and joins together regions called exons
Complex macromolecular machines called spliceosomes splice introns out of pre-mRNA
A "cap" is added to the 5' end of pre-mRNAs, and a poly(A) tail is added to their 3' end
The cap and tail serve as recognition signals for translation and protect the message from degradation by ribonucleases
RNA processing occurs in the nucleus
Ribosomes translate mRNAs into proteins with the help of adaptor molecules called transfer RNAs
In bacteria, an RNA is often transcribed and translated at the same time because there is no nucleus to separate these processes
In eukaryotes, transcription and translation of an RNA cannot occur together because transcription occurs in the _ and the translation occurs in the _
_ serve as the chemical bridge between the RNA message and the polypeptide product
Transfer RNAs (tRNAs)
Each _ carries an amino acid corresponding to the tRNA;s three-base-long anticodon
tRNAs have an L-shaped tertiary structure. One leg of the L contains the _ , which forms complementary base pairs with the mRNA codon. The other leg holds _.
anticodon; the amino acid specified by that codon
Enzymes called _ link the correct amino acid to the correct tRNA.
Because imprecise pairing wobble pairing can occur in the third position of the codon and anticodon, the approximately 40 types of tRNA in the cell are enough to translate ll 61 codons that code for amino acids
_ are large macromolecular machinces made of many proteins and RNAs
In the _ , the tRNA anticodon binds to a three-base-long mRNA codon to bring the correct amino acid into the ribosome
Peptide-bond formation by the ribosome is catalyzed by a _ (RNA), not an _ (protein)
Protein synthesis step one
An incoming aminoacyl tRNA occupies the A site
Protein synthesis step two
The growing polypeptide chain is transferred from a tRNA in the ribosome's P site to the amino acid bound to the tRNA in the A site, forming a peptide bond
Protein synthesis step three
The ribosome moves to the next codon on the mRNA, accomanied by ejection of the uncharged RNA from the E site
_ proteins help fold newly synthesized proteins
Most proteins need to be chemically modified after _(post-transitional modification) to activate the or target them to specific locations
Synthesis of RNA from DNA template
Are the DNAand RNA parallel or antiparallel? What direction is the template read?
RNA and DNA strands are antiparallel. The DNA template is "read" 3∙ → 5∙ (while RNA is being synthesized 5∙ → 3∙).
Ribonucleotide triphosphate. Like dNTP's but w hydroxyl on 2' carbon. Makes sugar ribose instead of deoxyribose in DNA.
NTPs with a base that matches a base on the DNA template is in place, RNA polymerase catalyzes a reaction the cleaves off two phosphtes and forms phosphordiester linkage between 3' end of growing mRN chain and the new ribonucleoside monophosphate.
Read by RNA polymerase
Its sequences matches the sequence the RNA transcribed from the template strand
A protein that must bind to polymerase before transcription can begin
RNA polymerase plus holoenzyme
Holoenzymes are a core enzyme, (RNA polymerase in this case) which contains the active site for catalysis and other required proteins (such as a sigma)
What do sigmas do? Bind to promotors (regions of DNA that promote the start of transcription), bind to any sequence of DNA. Specific types of sigmas initiate transcription of specific genes to be expressed to help cope with specific problems. Similar or identical bases on one strand 40
50 base pairs .
10 box/TATAAT centered 10 bases from the point where transcription starts
DNA located in direction of RNA polymerase moves during transcription is said to be _ from the point of reference.
DNA located in direction opposite of RNA polymerase moves during transcription is said to be _from the point of reference.
35 box, +1 Site (Where it begins)
In bacteria transcription can only begin when
sigma binds to the -35 and -10 boxes in the DNA.
when does initiation complete
sigma is released from promoter and RNA synthesis continues from DNA
Why is orientation important in bacteria?
orientation of promoter determines which 1. DNA strand is template and
2. which direction RNA polymerase will start synthesizing RNA
initiation and elongation
once holozyme is bound to a promoter RNA polymerase opens the helix, separating strands of DNA. the template strand is threaded through a channel leading to the active site of RNA polymerase where NTPs enter and diffuse to the active site, where they complement the DNA strand and a string of RNA develops, adding to 3' end each time
Is RNA polymerase exergonic/spontaneous?
Yes because NTPs are being bonded and they have very high potential energy
Channels in RNA polymerase
DNA enters one, exits one reunited with coding strand (double stranded), NTP enters one, NTPs bound into a growing RNA strand exit another
Stops in bacteria when RNA polymerase transcribes a DNA sequence called transcription-termination signal. its transcribes to form a short double helix held together by complementary base pairings to make hairpin.
How does hairpin mean termination?
The hairpin structure disrupts the interaction between RNA polymerase and the RNA transcipt, resulting in the seperation of the enzyme and its product
1. Predict how a mutation in a bacterial cell that deletes 3 nucleotides that are 10 nucleotides upstream from the transcription start site is likely to affect transcription
2. Predict how rotating the promoter sequence by 180 degrees will influence what is upstream and downstream DNA and which will be template which will be non-template
(1) Transcription would be reduced or absent because the missing nucleotides are in the −10 region, one of the two critical parts of the promoter. (2) (a) Upstream and downstream will be reversed since rotating the promoter will change the direction of transcription. (b) The template and non-template strands of DNA will be reversed.
One type; Three types each producing a different class of RNA
Proteins that associate with promotor
Sigma-different versions of sigma bind to different promoters; many basal transcription factors that assemble at the promoter as RNA polymerase follows
Typically -35 box and -10 box; More variable often TATA box -30
RNA processing bacteria;human
Rare; Extensive steps happen before RNA from nucleus exported to cytoplasm 1. enzyme-catalyzed addition of 5' cap on mRNAs 2. splicing (intron removal) by spliceosome to produce mRNA 3. enzyme-catalyzed addition of 3' poly(A) tail on mRNAs
Termination of transcription in eukaryotes
poly(A) signal near the end of each gene is transcribed. RNA downstream of poly(A) signal cut by enzyme as the polymerase continues with template. eventually at varying locations the RNA polyerae comes off the DNA template.
Termination In bacteria; In humans
transcription ends at a distinct site in each gene;transcription ends variable distances from the poly(A) signal
Translation (initiation, elongation, and termination) in bacteria
Initiation less complex, elongation and termination similar to eukaryotes.
Primary transcript in eukaryotes
pre-mRNA for protein coding genes; initial product of transcribing. must undergo extraneos RNA processing before functional mature RNA
If introns were absent what would the micrograph lok like?
There would be no loops. This is because the molecules would match up exactly if the DNA lacked introns.
Analogy of introns/exons
Eukaryotic genes don't just cary the sequence "Biology is my favorite course of all time." It carries "BIO1284035384242OGY IS MY
FAVOR1248109481294ITE CORSE..." The sections of numbers are noncoding sequences.
Regions of final RNA
regions in primary transcript but not in final RNA
Introns are removed/snipped in the nucleus by
snRNPs bind to start (5') of intron (GU) and complementary base within the intron (A). spliceosome is assembled from snRNPs and proteins, 5' end of intron cut and intron forms lariat w loop forming from base match (UA). 3' end is cut, releasing intron as lariat. phosphodiester bond forms between exons on either side.
what happens to excised introns
degraded to ribonucleoside monophosphates
catalyze splicing and rejoining in spliceosome / key role in translation
As soon as 5' end of eukaryotic pre-mRNA emerges from RNA polymerase
enzymes add 5' cap. modified guanine with 3 phosphate groups, enables ribosomes to bind to the mRNA protects the 5' end from RNA degrading enzymes (ribonucleases)
As enzyme cleaves 3' end of eukaryotic pre-mRNA downstream of poly(A) signal another enzyme adds 250 A nucleotides not encoded on DNA template strand
poly (A) tail. saves from enzymes and starts translation like 3' tail.
Untranslated regions of 5' and 3' end and are exons/ partly exons. stabalize mature RNA and regulate translation / also in bacteria
Example of exon or part of exon that doesnt code for amino acids. Explain how RNA of spliceosomes are able to recognize which area to recognize
(1) The 5∙ and 3∙ UTRs are either exons or parts of exons because they are present in the mRNA yet do not code for amino acids. (2) Base pairing between sequences in the primary transcripts and small nuclear RNAs (snRNAs) of snRNPs that make up the spliceosome allows recognition of the regions to be spliced.
similar in all domains of life
higher number of ribosomes the higher the
rate at which the cell synthesizes proteins
translation in bacteria
Transcription and translation are couples and occur simultaneously in bacteria becayse there is no nuclear envelope to seperate the two processes
ribosomes attach to mRNAs and begin syntheizing proteins before transcription is complete. when multiple ribosomes simultaneously translate one mRNA the structure is called a polyribosome so many copies of protein can be produced from a single mRNA
NH3+ / amino polypeptide terminal direction
5' end of mRNA
COOO- carboxyl polypeptide terminal direction
3' end of mRNA
what would the graph look like if the null hypothesis (radioactive amino acids will not be found in polypeptides) were correct?
If the amino acids stayed attached to the tRNAs, the gray line in the graph would stay high and the green line low. If the amino acids were transferred to some other cell component, the gray line would decline but the green line would be low.
if tRNA is absent protein synthesis did not occur.
chemical go-betweens that allow amino acids to interact with an mRNA template
describe where amino acids attaches and eplain the relaionship between anticodon or tRNA and a codon in an mRNA
(1) The amino acid attaches on the 3∙ end of the arm of the L-shaped structure that is farthest from the anticodon loop. (2) The anticodon is antiparallel in orientation to the mRNA codon, and it contains the complementary bases.
tRNA secondary structure IMG
stems created by hydrogen bonds between complementary base pairs and loops of unpaired bases. opposite of amino acid attachment side is anticodon
when tRNA attached to amino acid
group of three bases on a tRNA molecule that are complementary to an mRNA codon, which pair in antiparralel fashion
tRNA tertiary structures
L shape with anticodon on one end and amino sequence attached amino acid on the other end
require ATP, enzymes called aminoacyl-tRNA synthases catalyze he addition of amino acids to tRNAs- which biologist call "charging" a tRNA. for each of the 20 amino acids, there is a different amnc-tRNA synthase and one or more tRNAs
each aminoacyl-tRNA synthase has a binding site for a particular amino acid and a particular tRNA
subtle differences in shape and base sequence allow enzymes to match the correct tRNA to correct the amino acid
the hypothesis that some tRNA molecules can pair with more than one mRNA codon by tolerating particular types of nonstandard base pairing in the third base, so long as the first and second bases are correctly typed
In binding to tRNA, the nucleotide at the third base position in the mRNA codon can violate base pairing rules, leads to a degenerate code in which the 20 amino acids can be specified by more than one codon
complex of RNA molecules and proteins. During translation the large subunit is where peptide bond formation occurs, small holds the mRNA.
three tRNA bound to their corresponding mRNA codons by their anticodons. on the right there is an A site- for acceptor/aminoacyl
in the middle is pepitdyl/ peptide formation site which holds the growing peptide chain and E which has no amino acid attached and is about to leave the ribosome
1. an aminoacyl tRNA diffuses into a site if its anticodon matches the codon in the mRNA it stays in the ribosome. 2. a peptide bond forms between the aminoacyl tRNA in the A site and the growing polypeptide, held by p site tRNA 3. the ribosome moves down the mRNA by one codon, E tRNA leaves, p moves to E, A moves to P and A accepts another aminoacyl tRNA
each repeat of three step cycle grows the chain one amino acid
synthesis starts ate amino/N end and proceeds to carboxyl/C terminus
initiation, elongation, termination
find start codon is near but not at the 5' end of mRNA binds its S-D sequence (which is about 6 nucleotides upstream of the start codon) with corresponding sequence on ribosome subunit
proteins that help prepare the ribosome for translation and in binding the first aminoacyl tRNA to the ribosome which carries a methionine to the ribosome
initiation of translation simplified
recognition of start codon, assembly of ribosome, assistance from initation factors and the positioning of a methione-carrying initiation tRNA in the P site and the large ribosome subunit arrives to complete the complex
translation initiation completion
large subunit joins the complex, where tRNA assumes position on p-site of assembled ribosome
at the start E and A are empty, so an unmatched mRNA codon is exposed to the A site, it proceeds when a complementary aminoacyl tRNA binds to the codon in the A site
when both P and A ssites are occupied by tRNAs the amino acids on the tRNAs hit the ribosomes active site this is where
peptide bond formation, the most important thing in protein synthesis and by extent in the entire cell occurs
Ribosome enzyme or ribozyme?
Equally RNA and protein, but the active site is all RNA so its a ribozyme
the movement of a ribosome down a messenger RNA during translation
moves the ribosome in a 5' -> 3' direction relative to mRNA. Uses GTP every step of the way.
Moves uncharged tRNA into E site; moves the tRNA containing growin polypeptide into the P site; and opens the A site to expose a new codon. The empty tRNA that finds itself in E site is ejected from ribosome
1. aminoacyl tRNA arrives 2. form peptide-bond 3. translocation and repeat at each codon along the mRNA
Translation brought to end when
the translocating ribosome reaches one of the stop codons and a protein called a release factor recognizes the stop codon and fills the A site. stop codons are on the 3' region of RNA but never the very end.
Release factors fit tightly into the A site because the have the same shape and size as an aminoayl tRNA coming into a ribosome. Once in the A site, it catalyzes the hydrolysis of the bond that links the tRNA in the P site to the polypetide chain, freeing the polypeptide.
The newly synthesized polypeptide and uncharged tRNAs are realeased from the ribosome which seperates from the mRNA and the ribosome dissasociates to be ready for new start codons
Archea and Eukaryotic transcription and translation are
more similar than that of bacteria's
Make a protein fully functional
Determines a protein's function determined by the amino acid sequence on the polypetide chain, frequently guided by molecular chaperones
Often added to sugar or lipid groups may be critical to function or in kinases need the addition of a phosphate group to function/ be active
Why is it important that the initiator tRNA is in the P site instead of the A site? Why is it logical that a release factor has the same structure as aminoacyl tRNA
(1) Having the initiator tRNA in the P site is important because if the polypeptide chain is to grow, the A site must be empty to allow the next aminoacylated tRNA to come into the ribosome. (2) Because the release factor binds to the same A site in the ribosome normally occupied by an aminoacyl tRNA, the shape of the release factor and aminoacyl tRNA must be nearly identical to allow for a good fit.
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