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Bio L2 (PART 2 OF 3)

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nibbs06's version from 2016-06-27 00:19

TRANSCRIPTION

Question Answer
Most protein production takes place during _ of the cell cycle because _Go because the cell isn’t exerting energy in self-replication
In Euk’s, transcription takes place in thenucleus & mitochondria
The purpose of transcription is to create an _________ copy of _________RNA copy of a DNA template
The 3 main stages of transcription areInitiation, Elongation & Termination
In Initiation, a group of DNA binding proteins called _________ identify a _________ on the DNA strandTranscription Factors identify a Promoter
A Promoter isa sequence of DNA nucleotides that designate a beginning point for transcription
The Transcription Initiation Complex forms at thePromoter
The major enzyme of the Transcription Initiation Complex isRNA Polymerase
Where on the genome can transcription occur & how often certain sequences are transcribed is regulated bythe promoter
Variation's in the consensus sequence, the most common promoter nucleotide sequence, causesRNA polymerase to bind less tightly and less often to a given promoter, leading to transcription of the genes occurring less frequently
The Transcription Bubble is formed when theRNA Polymerase unzips the DNA double helix
In Elongation, RNA pol. transcribesjust one DNA nucleotide seq. into a complementary RNA nucleotide seq.
The transcribed strand is called theTemplate, Non-coding, (-) or Antisense Strand
The non-transcribed strand is called the _________, whichCoding or (+) Sense Strand; it protects its partner against degradation
RNA Pol moves along the DNA strand in the _’→_’ direction3’→5’
The new RNA strand is made in the _’→_’ direction5’ → 3’
Errors created in newly made RNA strands arenot called mutations; they aren’t transmitted to progeny
Proof-reading mechanisms in transcription, for euk’s arenon-existent!
Rho Proteins, in the termination phasehelp dissociate RNA Pol from the DNA template
Which strand of the DNA double helix is transcribed?Only the template strand
The Template strand is complementary to theCoding Strand & the mRNA
If transcription didn’t exist & the genome was translated directly into proteins,every cell would be the same
The main level of activation or deactivation of genes isTranscription
Regulation of gene expression, (Euk & Prok) occur at the level ofTranscription, via Activators & Repressors
Activators & Repressors bind tooperators & either activate or repress RNA Pol activity
Activators & Repressors are often allosterically regulated by small molecules, such ascAMP
Euk gene regulation adds complexities by involving the interaction ofmany genes and enhancer proteins
Enhancer areshort, non-coding DNA regions(Euk); similar to activators but act farther away from the promoter
The primary function of gene regulation in Prok’s is torespond to changes the cells environment (i.e., nutrients)
The primary function of gene regulation in multicellular organisms isto control the intra- and extracellular environments of the cell
Polycistronic isfound in prok mRNA that includes several genes in one single transcript
Monocistronic isfound in Euk mRNA that includes one gene per transcript
In the Jacob-Monod model of prok genetic regulationthe genetic unit consisting of the operator, promotor & genes that contributes to one prok mRNA is called the operon
An operon includesoperator, promoter and genes
Lac operon codes for enzymes thatallow E.coli to import & metabolize lactose when glucose isn’t sufficient
Lac Operon is activated ifglucose is scarce & lactose is present
Low glucose in E.Coli leads tohigh cAMP levels, which binds & activates CAP(catabolite activator protein), allowing it to bind to the CAP site that is adjacent & upstream to the promoter on the lac operon
A second regulatory site, besides the promoter, on the lac operon is called theOperator, which is located adjacent & downstream to the promoter
When there’s no lactose present in E.Coli, the lac repressorbinds to the operator site & prevents transcription of lac genes, thus preventing gene expression, this is called Gene Repression
When lactose is available in an E.Coli cell, it will bind tothe lac repressor protein, making it no longer able to bind to the operator site
Transcription of the lac genes proceeds whenthere’s no inhibition from the repressor protein; lactose is present
The presence of lactose can induce transcription of the lac operon onlywhen glucose isn’t present
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MODIFICATIONS/TRANSLATION

Question Answer
Epigenetic modification and gene regulation occurspost-transcription
What RNA molecules undergo post-transcriptional modification in prok’s?rRNA & tRNA (almost all mRNA is translated directly to protein)
What RNA molecules undergo post-transcriptional modification in Euk’s?all of the RNA
hnRNA is known aspre-mRNA & also the Primary Transcript (before modification)
Modifications of the mRNA serves 4 purposeshelping the translational machinery recognize the mRNA, protecting it from degradation, eliminating unnecessary sequences and providing a mechanism for variability in protein products produced from a single transcript.
Both ends of an mRNA sequence is modified; Even before the euk mRNA is fully transcribed, its5’ end gets capped via GTP (5’ cap) & the 3’ end gets polyadenylated; it gets a long series of Adenine nucleotides (Poly A Tail)
The 5’ Cap’s purpose is toprotect against degradation by exonucleases (enzymes that cleave nucleotides)
Splicing is a process to whichprimary transcripts are excised & discarded before leaving the nucleus
The portion of transcripts that are removed are calledIntrons, they’re degraded in the cell & they are much longer than exons
Splicing occurs whensnRNPs recognize nucleotide sequences @ the ends of the introns; they act as ribozymes. The snRNPs pull the ends of the introns together, forming an intron loop or lariat
snRNP’sare one of the few non-protein enzymes
The complex that’s formed from the association of the snRNPs & other assoc. proteins is called aspliceosome
Spliceosomes excisethe introns and joins the ends of the exons together to form the single/final mRNA strand
Euk’s exert control over gene expression & add to the protein product variety through the process ofalternative splicing
One of the major mechanisms in the regulation of Euk gene expression isAlternative Splicing
Alternative splicing, in Euk’s, allows the cell toincorporate different coding sequences into mature mRNA
Euk’s can create a variety of mRNA molecules fror translation from a single DNA coding sequence, viaAlternative splicing
The STOP codons areUAA, UAG & UGA
The START codon codes for the amino acidmethionine
The sequence of RNA nucleotides is written __’ → __’5’→3’
A polypeptide contains 100 amino acids. How many possible sequences are there for this polypeptide?20100
Wobble pairing isa flexibility in the bonding of the third base pair position between tRNA & mRNA; the first two base pairs in the codon & anti codon must be strictly complimentary (A w/ U & C w/ G); this is why multiple codons can code for the same amino acid
Ribosome subunits are made fromrRNA & many separate proteins
Prokaryotic Ribosome size issmaller than Euk; 30S & 50S, w/ a combined size of 70S
Eukaryotic ribosome size is40S & 60S, w/ a combined size of 80S
Ribosomes are made in a special organelle called thenucleolus (Prok’s don’t have this but make it similarly)
After post-transcriptional processing, how does the 5’ end attach to the small ribosome subunit?via Initiation Factors (co-factor proteins)
A tRNA w/ the 5’-CAU-3’ anticodon, sequesters the amino acid methionine & moves it into theP-Site
The signal for the large subunit to join & form the initiation complex isMeth seq moving to the P-Site
Most of the translational regulation occurs during the _________ stageInitiation
During the Elongation Phase, the ribosome moves down the mRNA in a __’ → __’5’→3’ matching each codon to a complementary tRNA anticodon
Once the Met-tRNA is @ the P-Site, a new tRNA w/ its corresponding Amino Acid attaches to theA Site
The C-terminus of Met, attaches to the N-terminus of the amino acid @ the A site in a _________ reaction, forming a _________Dehydration; forming a Peptide bond
When a non-sense codon (stop codon) reaches the A-site, _________ bind to the A-site, allowing a _________ molecule to _________Release Factors(co-factor proteins); water moleucles; add to the end of the polypeptide chain
Initiation Phase of TranslationMet codon is paired & moves the P Site of tRNA
Elongation Phase of Translationinitiation complex forms; ribosome moves down the mRNA 5’→3’, adding the second AA onto the A Site; after lengthening the polypeptide, the ribosome shifts towards the 3’& the tRNA that carried the Methionine moves to the E Site, which can exit the ribosome. The tRNA carrying the newly formed dipeptide, leaves the A Site & goes to the P Site. Elongation repeates until a STOP codon reaches the P Site.
Termination Phase of Translationribosome reaches STOP codon @ A Site. Release Factors bind to the A Site, allowing water molecules to bind to the end of the polypeptide chain, thus freeing it from tRNA & ribosome
Mechanisms for regulating gene expression by affecting which of the translational products will become functional proteins is known asPost-Translational Modification
Proteins enjected into the ER lumen are destined to becomeMembrane bound proteins of the nuclear envelope, ER, golgi, lysosomes or plasma membrane, or often secreted from the cell
The destination of the polypeptide occurs via a 20 amino acid sequence called asignal peptide; it may direct a free floating ribosome to attach to the ER
Signal Peptide is recognized by a protein-RNASignal Recognition Particle (SR P)
The protein that carries the whole ribosome complex to the receptor protein on the ER, is theSignal Recognition Particle (SR P)
memorize

DNA REPLICATION

Question Answer
DNA replication takes place during the _ phase & makes 2 copies to be available for the _________ phaseS phase of interphase & M Phase – 1 for each resultant cell
The purpose of DNA replication is tomake 2 copies of the genome for each of the cells during cell division
Replication occurs atthe Origin of Replication, which is in the middle of the chromosome, not beginning
Each copy has 1 strand from the original DNA & 1 newly synthesized strand, this is known assemiconservative replication
Origin of replication in Proks vs Euk’s varies in thatEuk’s have many OR’s & Prok’s only have one
Epigenetic markers regulate how & where replication begins, bydesignating the origins of replication
At the origin of replication, 2 _________ begin in opposite directions along the chromosomeReplisomes (bidirectional)
Replisomes attach onto the chromosome at theReplication Fork
Each chromosome of Euk DNA is replicated in discrete segments calledReplication Units or Replicons
The enzymes included in the replisomes areDNA Helicase, DNA Polymerase, Primase & DNA Ligase
DNA Helicaseunwinds the double helix
DNA Polymerasepairs free-floating deoxynucleotides with the exposed strand; it can only add nucleotides to an existing strand & it cannot initiate a new strand! Relies on Primase
DNA Polymearse reads in the _________ direction and creates the new strand in the _________ direction3’→5’(upstream) & 5’→3’
Primasean RNA Polymerase that creates an RNA primer(~10ribonucleotides in length) to allow DNA Polymerase to add deoxynucleotides onto the primer & thus creates a new strand
DNA LigaseJoins okazaki fragments together
The strand that’s looped around the replisome because _________ & doesn’t fold back on itself because of _________DNA Pol reads in one strand so both strands must be oriented the same way; SSB (Strand Binding Tetramer Proteins)
Explain DNA replication processAt the origin of replication, DNA Helicase unwinds the strand, giving us a leading & lagging strand. Primase creates RNA Primers to initiate the lagging strand. DNA Pol synthesizes the new DNA strands by pairing the leading & lagging strands w. complementary deoxynucleotides. The lagging strand is looped around the replisome to give it the same orientation as the leading strand, since DNA Pol reads in only one direction, the 3’→5’ direction & it then creates the new complementary strand in the 5’→3’ direction. RNA primer gaps are filled by DNA Pol. & lastly, okazaki fragments are joined together by DNA Ligase
The ends of Euk’ chromosomes haveTelomeres; repeated 6 nucleotide units from 100 to 1000 units long that protect the ends of chromosomes
Telomerasesomewhat counteracts the shortening effect of replication on telomeres; it catalyzes the lengthening of telomeres
Replication of DNA in humans is fast because ofmultiple Origins of Replication
New strands are proof read & repairs of any mismatched nucleotides are made viaExonuclease subunit of DNA PoL
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MITOSIS

Question Answer
Mitosis isnuclear division w/out genetic change
Prophasechromatin condenses into chromosome. The two identical copies of duplicated chromosomes (sister chromatids) are joined near their centers, @ their centromeres. Centrioles, located in the centrosomes, move to opposite poles of the cell. The nucleolus & the nucleus disappear as the nuclear envelope breaks down. The Spindle Apparatus begins to form.
Spindle Apparatus consists ofAsters, microtubules that radiate from the centrioles. Kinetochore Microtubules, growing from the centromeres & spindle microtubules, connect the two centrioles.
Kinetochore is astructure of protein & DNA located at the centromere of the joined chromatid of each chromosome
Metaphasechromosomes align along the equator of the cell
Anaphasesister chromatids split (disjunction) at their attaching centromeres & segregate to opposite sides of the cell via the shortening of the kinetochore microtubules
Cytokinesisthe separation of the cellular cytoplasm due to constriction of microfilaments around the center of the cell; this may or may not commence towards the end of anaphase
Telophasethe nuclear membrane reforms, then nucleolus reforms. Chromosomes condense and become hard to see under a microscope. Cytokinesis continues, resulting in two identical daughter cells
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